diff --git a/.github/workflows/modules/append_module.lua b/.github/workflows/modules/append_module.lua
new file mode 100644
index 00000000..e45cb640
--- /dev/null
+++ b/.github/workflows/modules/append_module.lua
@@ -0,0 +1,3 @@
+setenv("INSIDE_GITHUB_ACTIONS", "true")
+-- Interfere with PATH so Lmod keeps a record
+prepend_path("PATH", "/snap/bin")
diff --git a/.github/workflows/modules/prepend_module.lua b/.github/workflows/modules/prepend_module.lua
new file mode 100644
index 00000000..e45cb640
--- /dev/null
+++ b/.github/workflows/modules/prepend_module.lua
@@ -0,0 +1,3 @@
+setenv("INSIDE_GITHUB_ACTIONS", "true")
+-- Interfere with PATH so Lmod keeps a record
+prepend_path("PATH", "/snap/bin")
diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index f543835c..509f71f4 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -11,11 +11,17 @@ if [ -z ${EXPECTED_EASYBUILD_VERSION} ]; then
   exit 1
 fi
 
+if [ -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
+  echo "\$EESSI_SOFTWARE_SUBDIR_OVERRIDE has to be set (e.g., x86_64/intel/haswell) so we can do well defined string comparison for the architecture."
+  exit 1
+fi
+
 # initialize assert framework
 if [ ! -d assert.sh ]; then
   echo "assert.sh not cloned."
   echo ""
   echo "run \`git clone https://github.com/lehmannro/assert.sh.git\`"
+  echo "(see workflow file that calls this script for how to only clone specific commit if you are worried about security)"
   exit 1
 fi
 . assert.sh/assert.sh
@@ -28,9 +34,13 @@ for shell in ${SHELLS[@]}; do
   echo  RUNNING TESTS FOR SHELL: $shell
   echo = | awk 'NF += (OFS = $_) + 100'
   if [[ ! " ${TEST_SHELLS[*]} " =~ [[:space:]]${shell}[[:space:]] ]]; then
-    ### EXCEPTION FOR CSH ###
     echo -e "\033[33mWe don't now how to test the shell '$shell', PRs are Welcome.\033[0m" 
   else
+    if [ "$shell" = "csh" ]; then
+      # make sure our .cshrc is empty before we begin as we will clobber it
+      [ -f ~/.cshrc ] && mv ~/.cshrc ~/.cshrc_orig
+    fi
+
     # TEST 1: Source Script and check Module Output
     expected="Module for EESSI/$EESSI_VERSION loaded successfully"
     assert "$shell -c 'source init/lmod/$shell' 2>&1 " "${expected}"
@@ -45,11 +55,12 @@ for shell in ${SHELLS[@]}; do
     else
       MODULE_SECTIONS=($($shell -c "source init/lmod/$shell 2>/dev/null; module ov 2>&1 | grep -e '---'"))
     fi
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/modules/all"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/modules/all"
     assert_raises 'echo "${MODULE_SECTIONS[1]}" | grep -E "$PATTERN"'
+    echo "${MODULE_SECTIONS[1]}" "$PATTERN"
 
     # TEST 3: Check if module overviews second section is the EESSI init module
-    assert "echo ${MODULE_SECTIONS[4]}" "/cvmfs/software.eessi.io/versions/$EESSI_VERSION/init/modules"
+    assert "echo ${MODULE_SECTIONS[4]}" "/cvmfs/software.eessi.io/init/modules"
 
     # TEST 4: Load EasyBuild module and check version
     # eb --version outputs: "This is EasyBuild 5.1.1 (framework: 5.1.1, easyblocks: 5.1.1) on host ..."
@@ -69,12 +80,45 @@ for shell in ${SHELLS[@]}; do
       EASYBUILD_PATH=$($shell -c "source init/lmod/$shell 2>/dev/null; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; which eb")
     fi
     # escape the dots in ${EASYBUILD_VERSION}
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
     echo "$EASYBUILD_PATH" | grep -E "$PATTERN"
     assert_raises 'echo "$EASYBUILD_PATH" | grep -E "$PATTERN"'
+    echo "$EASYBUILD_PATH" "$PATTERN"
+
+    # TEST 6 and 7: Check the various options (EESSI_DEFAULT_MODULES_APPEND, EESSI_DEFAULT_MODULES_APPEND, EESSI_EXTRA_MODULEPATH) all work
+    if [ "$shell" = "csh" ]; then
+      echo "setenv EESSI_DEFAULT_MODULES_APPEND append_module" > ~/.cshrc
+      echo "setenv EESSI_DEFAULT_MODULES_PREPEND prepend_module" >> ~/.cshrc
+      echo "setenv EESSI_EXTRA_MODULEPATH .github/workflows/modules" >> ~/.cshrc
+      echo "source init/lmod/$shell" >> ~/.cshrc
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'echo $MODULEPATH')
+    elif [ "$shell" = "fish" ]; then
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+    else
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+    fi
+    LMOD_SYSTEM_DEFAULT_MODULES_PATTERN='^prepend_module:.*:append_module$'
+    echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" AND "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"
+    assert_raises 'echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" | grep -E "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"'
+    if [ "$shell" = "fish" ]; then
+      MODULEPATH_PATTERN='\.github/workflows/modules$'
+    else
+      MODULEPATH_PATTERN=':\.github/workflows/modules$'
+    fi
+    echo "$TEST_MODULEPATH" AND "$MODULEPATH_PATTERN"
+    assert_raises 'echo "$TEST_MODULEPATH" | grep -E "$MODULEPATH_PATTERN"'
 
     # End Test Suite
     assert_end "source_eessi_$shell"
+
+    if [ "$shell" = "csh" ]; then
+      # Restore our .cshrc
+      [ -f ~/.cshrc_orig ] && mv ~/.cshrc_orig ~/.cshrc
+    fi
+
   fi
 done
 
diff --git a/.github/workflows/tests_init_module.yml b/.github/workflows/tests_init_module.yml
index b4d31435..902c31e3 100644
--- a/.github/workflows/tests_init_module.yml
+++ b/.github/workflows/tests_init_module.yml
@@ -46,8 +46,13 @@ jobs:
             sed -i "s/__EESSI_VERSION_DEFAULT__/${{matrix.EESSI_VERSION}}/g" init/lmod/${shell}
           done
 
-      - name: Clone assert.sh script
-        run: git clone https://github.com/lehmannro/assert.sh.git
+      - name: Clone assert.sh at pinned commit
+        run: |
+          ASSERT_COMMIT_SHA=fe359e341670f1e8e86a3804ca00e5a3ebc30fa4
+          git clone --no-checkout https://github.com/lehmannro/assert.sh.git
+          cd assert.sh
+          git fetch --depth 1 origin $ASSERT_COMMIT_SHA
+          git checkout $ASSERT_COMMIT_SHA
 
       - name: Install missing shells
         run: |
@@ -55,9 +60,20 @@ jobs:
           sudo apt install zsh ksh fish tcsh
           echo "# INIT ZSH" > ~/.zshrc
 
-      - name: Run tests for available shells
+      - name: Run tests for available shells without system Lmod
         run: |
+          export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
+          export EESSI_VERSION=${{matrix.EESSI_VERSION}}
+          export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
+          .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"
+      - name: Run tests for available shells with system Lmod
+        run: |
+          # We also want to perform the same test when there is an Lmod version available on the system
+          sudo apt install lmod
+          source /usr/share/lmod/lmod/init/bash
+          export MODULEPATH=/usr/share/lmod/lmod/modulefiles
+          module avail
+          export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}
           export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
           .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"
-
diff --git a/init/lmod/bash b/init/lmod/bash
index daba8351..2110400d 100644
--- a/init/lmod/bash
+++ b/init/lmod/bash
@@ -1,19 +1,91 @@
+#!/usr/bin/env bash
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Assumptions:
+# - EESSI accessible under $EESSI_CVMFS_REPO or /cvmfs/software.eessi.io
+#   - expected to be true as this file is also meant to be shipped under that location
+#   - Lmod must the shipped in the repository in the correct location
+#
+# Options:
+# - The script listens to environment variables so that it can be silently configured by a site
+#   - EESSI_CVMFS_REPO: perform the initialisation from a respository other than /cvmfs/software.eessi.io
+#   - EESSI_VERSION: loads a specific EESSI version ignoring the default in the file
+#   - EESSI_DEFAULT_MODULES_PREPEND: environment variable allows you to prepend modules to the defaults (loaded last)
+#   - EESSI_DEFAULT_MODULES_APPEND: environment variable allows you to append modules to the defaults (loaded first)
+#   - EESSI_EXTRA_MODULEPATH: environment variable allows a site to append to MODULEPATH (lower priority than EESSI MODULEPATH)
+#
+# Other options that can be set to influence the end result:
+# - The EESSI module also listens to environment variables so that it can be silently configured by a site
+#   - EESSI_MODULE_FAMILY_NAME: use the value of the environment variable to set an Lmod family for the EESSI module
+#   - EESSI_MODULE_STICKY: make the EESSI module sticky
+#   - EESSI_MODULE_UPDATE_PS1: have the EESSI module update PS1 to give a prompt that is prepended with "{EESSI/...} "
+#
+# Effects:
+# - Should always succeed
+# - Initialises Lmod from specific version of EESSI
+#   - Clobbers any existing Lmod configuration
+#   - Some special environment variables that are internal to Lmod (__LMOD_REF_COUNT_MODULEPATH and
+#     _ModuleTable001_) are used to force a hard reset of an existing Lmod installation. This
+#     approach may be brittle.
+# - Then loads module EESSI/... to initialise EESSI
+#   - use `module show EESSI/...` to see the environment variables set by the EESSI module
+#
+# Reverting the effects:
+# - EESSI initialisation via `module unload EESSI/...`
+# - Lmod initialisation cannot be undone
+
 # Choose an EESSI CVMFS repository
 EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
-# Choose an EESSI version
-EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
+
+# Choose an EESSI version (the default is only used if the EESSI_VERSION environment variable is not provided)
+# (Note: in the repository which is home to this file a template value __EESSI_VERSION_DEFAULT__ is present in
+#  the line below which is replaced within our deployment pipeline.)
+EESSI_VERSION_DEFAULT="${__EESSI_VERSION_USED_FOR_INIT:-__EESSI_VERSION_DEFAULT__}"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Path to top-level module tree
-export MODULEPATH="${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-. "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash"
+# On the first run we want to record the EESSI version used for init as an environment variable so that if a different
+# version of this script is called (e.g, for a a different EESSI version) it retains a memory which EESSI
+# version was actually used in the initialisation. This is useful as __Init_EESSI_Default_Modules used below will
+# be defined on the first call and Lmod initialisation will not happen twice.
+# This sets the value only on first execution, if the variable already exists in the environment
+# the original value is retained.
+export __EESSI_VERSION_USED_FOR_INIT="${__EESSI_VERSION_USED_FOR_INIT:-${EESSI_VERSION}}"
+
+# LMOD_SYSTEM_DEFAULT_MODULES are used by Lmod to load a default set of modules in the scenario
+# - where we initialise Lmod (the if part of the clause below)
+# - where we reset Lmod (the else part of the clause below)
+# This means that if we call this script twice we will get the same end result: an Lmod installation
+# with a set of default modules loaded.
+#
+# We also allow the ability to predefine elsewhere the default list of modules to load (colon separated):
+# - EESSI_DEFAULT_MODULES_PREPEND environment variable allows you to prepend modules (loaded last)
+# - EESSI_DEFAULT_MODULES_APPEND environment variable allows you to append modules (loaded first)
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
+export LMOD_SYSTEM_DEFAULT_MODULES
+
+if [ -z "$__Init_EESSI_Default_Modules" ]; then
+    export __Init_EESSI_Default_Modules=1;
+
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    LMOD_EESSI_VERSION=${EESSI_VERSION/2023.06/2025.06}
 
-if [ -z "$__Init_Default_Modules" ]; then
-   export __Init_Default_Modules=1;
+    # Lmod may have been initialised so we need to clear some internal variables to allow for a full reset
+    # - make it forget about the system set MODULEPATH
+    unset __LMOD_REF_COUNT_MODULEPATH
+    # - and clear out any memory Lmod might have
+    unset _ModuleTable001_
 
-   ## ability to predefine elsewhere the default list
-   LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
-   export LMOD_SYSTEM_DEFAULT_MODULES
-   module --initial_load --no_redirect restore
+    # Path to top-level module tree
+    # - EESSI_EXTRA_MODULEPATH environment variable allows a site to append to MODULEPATH (lower priority than EESSI MODULEPATH)
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules${EESSI_EXTRA_MODULEPATH:+:$EESSI_EXTRA_MODULEPATH}"
+    . "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash"
+    module --initial_load --no_redirect restore
 else
-   module refresh
+    module reset
 fi
diff --git a/init/lmod/csh b/init/lmod/csh
index 2adb314c..a10836d1 100644
--- a/init/lmod/csh
+++ b/init/lmod/csh
@@ -1,24 +1,70 @@
+#!/usr/bin/env csh
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
-if (! $?EESSI_CVMFS_REPO) then
+if ( ! $?EESSI_CVMFS_REPO) then
     set EESSI_CVMFS_REPO = "/cvmfs/software.eessi.io"
 endif
-# Choose an EESSI version
-setenv EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
-if (! $?EESSI_VERSION) then
-    set EESSI_VERSION = "${EESSI_VERSION_DEFAULT}"
+
+# Choose an EESSI version (default is used if EESSI_VERSION is not provided)
+if ( ! $?__EESSI_VERSION_USED_FOR_INIT ) then
+    set EESSI_VERSION_DEFAULT = "__EESSI_VERSION_DEFAULT__"
+else
+    set EESSI_VERSION_DEFAULT = "$__EESSI_VERSION_USED_FOR_INIT"
+endif
+if ( ! $?EESSI_VERSION ) then
+    set EESSI_VERSION = "$EESSI_VERSION_DEFAULT"
+endif
+# On first run, record the EESSI version used for init as an environment variable.
+# We use setenv to ensure it is available to child processes (equivalent to export).
+if ( ! $?__EESSI_VERSION_USED_FOR_INIT ) then
+    setenv __EESSI_VERSION_USED_FOR_INIT "$EESSI_VERSION"
 endif
-# Path to top-level module tree
-setenv MODULEPATH "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-source "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"
 
-if (! $?__Init_Default_Modules ) then
-    setenv __Init_Default_Modules 1
+# ability to predefine elsewhere the default list (with options to append or prepend)
+set LMOD_SYSTEM_DEFAULT_MODULES = "EESSI/${EESSI_VERSION}"
+if ( $?EESSI_DEFAULT_MODULES_PREPEND ) then
+    set LMOD_SYSTEM_DEFAULT_MODULES = "${EESSI_DEFAULT_MODULES_PREPEND}:${LMOD_SYSTEM_DEFAULT_MODULES}"
+endif
+if ( $?EESSI_DEFAULT_MODULES_APPEND ) then
+    set LMOD_SYSTEM_DEFAULT_MODULES = "${LMOD_SYSTEM_DEFAULT_MODULES}:${EESSI_DEFAULT_MODULES_APPEND}"
+endif
+setenv LMOD_SYSTEM_DEFAULT_MODULES "${LMOD_SYSTEM_DEFAULT_MODULES}"
+
+if ( ! $?__Init_EESSI_Default_Modules ) then
+    setenv __Init_EESSI_Default_Modules 1
 
-    # ability to predefine elsewhere the default list
-    if (! $?LMOD_SYSTEM_DEFAULT_MODULES) then
-        setenv LMOD_SYSTEM_DEFAULT_MODULES "EESSI/${EESSI_VERSION}"
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    set LMOD_EESSI_VERSION = "${EESSI_VERSION}"
+    if ( "${LMOD_EESSI_VERSION}" == "2023.06" ) then
+      set LMOD_EESSI_VERSION = "2025.06"
     endif
+
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    unsetenv __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    unsetenv _ModuleTable001_
+    # Path to top-level module tree
+    set modulepath = "${EESSI_CVMFS_REPO}/init/modules"
+    if ( $?EESSI_EXTRA_MODULEPATH ) then
+      # Now that we know it exists, check IF it is not empty
+      if ( "$EESSI_EXTRA_MODULEPATH" != "" ) then
+        set modulepath = "${modulepath}:${EESSI_EXTRA_MODULEPATH}"
+      endif
+    endif
+    setenv MODULEPATH "$modulepath"
+    source "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"
+
     module --initial_load --no_redirect restore
 else
-    module refresh
+    module reset
 endif
diff --git a/init/lmod/fish b/init/lmod/fish
index 9e595441..881e6262 100644
--- a/init/lmod/fish
+++ b/init/lmod/fish
@@ -1,18 +1,62 @@
+#!/usr/bin/env fish
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
 set EESSI_CVMFS_REPO (set -q EESSI_CVMFS_REPO; and echo "$EESSI_CVMFS_REPO"; or echo "/cvmfs/software.eessi.io")
+
 # Choose an EESSI version
-set EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
-set EESSI_VERSION (set -q EESSI_VERSION; and echo "$EESSI_VERSION"; or echo "$EESSI_VERSION_DEFAULT")
-# Path to top-level module tree
-set -x MODULEPATH "$EESSI_CVMFS_REPO"/versions/"$EESSI_VERSION"/init/modules
-. "$EESSI_CVMFS_REPO"/versions/"$EESSI_VERSION"/compat/linux/(uname -m)/usr/share/Lmod/init/fish
-
-if test -z "$__Init_Default_Modules"
-	export __Init_Default_Modules=1;
-
-	## ability to predefine elsewhere the default list
-	set -x LMOD_SYSTEM_DEFAULT_MODULES (set -q LMOD_SYSTEM_DEFAULT_MODULE; and echo "$LMOD_SYSTEM_DEFAULT_MODULE"; or echo "EESSI/$EESSI_VERSION")
-	module --initial_load --no_redirect restore
+if not set -q __EESSI_VERSION_USED_FOR_INIT
+    set EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
+else
+    set EESSI_VERSION_DEFAULT "$__EESSI_VERSION_USED_FOR_INIT"
+end
+if not set -q EESSI_VERSION
+    set EESSI_VERSION "$EESSI_VERSION_DEFAULT"
+end
+
+# Record version used for init; -x exports it to the environment
+if not set -q __EESSI_VERSION_USED_FOR_INIT
+    set -x __EESSI_VERSION_USED_FOR_INIT "$EESSI_VERSION"
+end
+
+# ability to predefine elsewhere the default list (with options to append or prepend)
+set LMOD_SYSTEM_DEFAULT_MODULES "EESSI/$EESSI_VERSION"
+if set -q EESSI_DEFAULT_MODULES_PREPEND
+    set LMOD_SYSTEM_DEFAULT_MODULES "$EESSI_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
+end
+if set -q EESSI_DEFAULT_MODULES_APPEND
+    set LMOD_SYSTEM_DEFAULT_MODULES "$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_DEFAULT_MODULES_APPEND"
+end
+set -x LMOD_SYSTEM_DEFAULT_MODULES $LMOD_SYSTEM_DEFAULT_MODULES
+
+if test -z "$__Init_EESSI_Default_Modules"
+    set -x __Init_EESSI_Default_Modules 1
+
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    set LMOD_EESSI_VERSION (string replace 2023.06 2025.06 -- $EESSI_VERSION)
+
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    set -e __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    set -e _ModuleTable001_
+    # Path to top-level module tree
+    set modulepath "$EESSI_CVMFS_REPO/init/modules"
+    if set -q EESSI_EXTRA_MODULEPATH; and test -n "$EESSI_EXTRA_MODULEPATH"
+        set modulepath "$modulepath:$EESSI_EXTRA_MODULEPATH"
+    end
+    set -x MODULEPATH $modulepath
+    . "$EESSI_CVMFS_REPO"/versions/"$LMOD_EESSI_VERSION"/compat/linux/(uname -m)/usr/share/Lmod/init/fish
+
+    module --initial_load --no_redirect restore
 else
-	module refresh
+    module reset
 end
diff --git a/init/lmod/ksh b/init/lmod/ksh
index ebf4c0ca..37c3caff 100644
--- a/init/lmod/ksh
+++ b/init/lmod/ksh
@@ -1,19 +1,48 @@
+#!/usr/bin/env ksh
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
 EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
-# Choose an EESSI version
-EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
+
+# Choose an EESSI version (the default is only used if the EESSI_VERSION environment variable is not provided)
+EESSI_VERSION_DEFAULT="${__EESSI_VERSION_USED_FOR_INIT:-__EESSI_VERSION_DEFAULT__}"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Path to top-level module tree
-export MODULEPATH="${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-. "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/ksh"
+# On the first run we want to record the EESSI version used for init as an environment variable so that if a different
+# version of this script is called (e.g, for a a different EESSI version) it retains a memory which EESSI
+# version was actually used in the initialisation. This is useful as __Init_EESSI_Default_Modules used below will
+# be defined on the first call and Lmod initialisation will not happen twice.
+# This sets the value only on first execution, if the variable already exists in the environment
+# the original value is retained.
+export __EESSI_VERSION_USED_FOR_INIT="${__EESSI_VERSION_USED_FOR_INIT:-${EESSI_VERSION}}"
+
+# ability to predefine elsewhere the default list (with options to append or prepend)
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
+export LMOD_SYSTEM_DEFAULT_MODULES
+   
+if [ -z "$__Init_EESSI_Default_Modules" ]; then
+    export __Init_EESSI_Default_Modules=1;
+
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    LMOD_EESSI_VERSION=${EESSI_VERSION/2023.06/2025.06}
 
-if [ -z "$__Init_Default_Modules" ]; then
-   export __Init_Default_Modules=1;
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    unset __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    unset _ModuleTable001_
+    # Path to top-level module tree
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules${EESSI_EXTRA_MODULEPATH:+:$EESSI_EXTRA_MODULEPATH}"
+    . "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/ksh"
 
-   ## ability to predefine elsewhere the default list
-   LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
-   export LMOD_SYSTEM_DEFAULT_MODULES
-   module --initial_load --no_redirect restore
+    module --initial_load --no_redirect restore
 else
-   module refresh
+    module reset
 fi
diff --git a/init/lmod/zsh b/init/lmod/zsh
index dfdff0c7..f7c0fc25 100644
--- a/init/lmod/zsh
+++ b/init/lmod/zsh
@@ -1,19 +1,48 @@
+#!/usr/bin/env zsh
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
 EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
-# Choose an EESSI version
-EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
+
+# Choose an EESSI version (the default is only used if the EESSI_VERSION environment variable is not provided)
+EESSI_VERSION_DEFAULT="${__EESSI_VERSION_USED_FOR_INIT:-__EESSI_VERSION_DEFAULT__}"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Path to top-level module tree
-export MODULEPATH="${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-. "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/zsh"
+# On the first run we want to record the EESSI version used for init as an environment variable so that if a different
+# version of this script is called (e.g, for a a different EESSI version) it retains a memory which EESSI
+# version was actually used in the initialisation. This is useful as __Init_EESSI_Default_Modules used below will
+# be defined on the first call and Lmod initialisation will not happen twice.
+# This sets the value only on first execution, if the variable already exists in the environment
+# the original value is retained.
+export __EESSI_VERSION_USED_FOR_INIT="${__EESSI_VERSION_USED_FOR_INIT:-${EESSI_VERSION}}"
+
+# ability to predefine elsewhere the default list (with options to append or prepend)
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
+export LMOD_SYSTEM_DEFAULT_MODULES
+
+if [ -z "$__Init_EESSI_Default_Modules" ]; then
+    export __Init_EESSI_Default_Modules=1;
+
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    LMOD_EESSI_VERSION=${EESSI_VERSION/2023.06/2025.06}
 
-if [ -z "$__Init_Default_Modules" ]; then
-   export __Init_Default_Modules=1;
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    unset __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    unset _ModuleTable001_
+    # Path to top-level module tree
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules${EESSI_EXTRA_MODULEPATH:+:$EESSI_EXTRA_MODULEPATH}"
+    . "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/zsh"
 
-   ## ability to predefine elsewhere the default list
-   LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
-   export LMOD_SYSTEM_DEFAULT_MODULES
-   module --initial_load --no_redirect restore
+    module --initial_load --no_redirect restore
 else
-   module refresh
+    module reset
 fi