diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index ed71ee5b53..d514293706 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -95,7 +95,19 @@ elseif (os.getenv("NESSI_SITE_INSTALL") ~= nil) then
   if ((os.getenv("NESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("NESSI_USER_INSTALL") ~= nil)) then
     LmodError("You cannot use NESSI_SITE_INSTALL in combination with any other NESSI_*_INSTALL environment variables")
   end
-  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+  site_install = os.getenv("NESSI_SITE_INSTALL")
+  site_modulepath = nil
+  if (site_install ~= nil) then
+    -- Check the folder exists
+    if not isDir(site_install) then
+      LmodError("The location of NESSI_SITE_INSTALL (" .. site_install .. ") does not exist or is not a folder")
+    end
+    if (mode() == "load") then
+      LmodMessage("Configuring for use of NESSI_SITE_INSTALL under " .. site_install)
+    end
+    easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), site_install)
+    site_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
+  end
 else
   -- Deal with user and project installs
   project_install = os.getenv("NESSI_PROJECT_INSTALL")
diff --git a/easystacks/pilot.nessi.no/2023.06/rebuilds/20240519-eb-4.9.1-rebuild-NESSI-extend-module.yml b/easystacks/pilot.nessi.no/2023.06/rebuilds/20240519-eb-4.9.1-rebuild-NESSI-extend-module.yml
new file mode 100644
index 0000000000..fbb323ff2e
--- /dev/null
+++ b/easystacks/pilot.nessi.no/2023.06/rebuilds/20240519-eb-4.9.1-rebuild-NESSI-extend-module.yml
@@ -0,0 +1,5 @@
+# 2024-05-19
+# Rebuild NESSI-extend/2023.06-easybuild
+# The current version does not handle NESSI_SITE_INSTALL correctly.
+easyconfigs:
+  - EESSI-extend-2023.06-easybuild.eb
diff --git a/eessi_container.sh b/eessi_container.sh
index ad9397318a..c9ed97e5c6 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -625,7 +625,6 @@ if [[ "${ACCESS}" == "rw" ]]; then
   EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
 
   EESSI_WRITABLE_OVERLAY="container:fuse-overlayfs"
-  EESSI_WRITABLE_OVERLAY+=" -o lowerdir=/cvmfs_ro/${repo_name}"
   if [[ ! -z ${LOWER_DIRS} ]]; then
     # need to convert ':' in LOWER_DIRS to ',' because bind mounts use ',' as
     # separator while the lowerdir overlayfs option uses ':'