diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index 57c078f511..2c7622b45a 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -92,7 +92,12 @@ if [[ "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
 fi
 
 echo ">> Determining software subdirectory to use for current build host..."
-export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
+if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
+  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
+  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
+else
+  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
+fi
 
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
 # $EESSI_SILENT - don't print any messages
diff --git a/build_container.sh b/build_container.sh
index f8e9c6bf59..bddd3dfffc 100755
--- a/build_container.sh
+++ b/build_container.sh
@@ -43,6 +43,13 @@ fi
 export EESSI_PILOT_READONLY="container:cvmfs2 pilot.eessi-hpc.org /cvmfs_ro/pilot.eessi-hpc.org"
 export EESSI_PILOT_WRITABLE_OVERLAY="container:fuse-overlayfs -o lowerdir=/cvmfs_ro/pilot.eessi-hpc.org -o upperdir=$EESSI_TMPDIR/overlay-upper -o workdir=$EESSI_TMPDIR/overlay-work /cvmfs/pilot.eessi-hpc.org"
 
+# pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)
+if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
+    export SINGULARITYENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+    # also specify via $APPTAINERENV_* (future proof, cfr. https://apptainer.org/docs/user/latest/singularity_compatibility.html#singularity-environment-variable-compatibility)
+    export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+fi
+
 if [ "$SHELL_OR_RUN" == "shell" ]; then
     # start shell in Singularity container, with EESSI repository mounted with writable overlay
     echo "Starting Singularity build container..."
diff --git a/run_in_compat_layer_env.sh b/run_in_compat_layer_env.sh
index 118aac65d5..561a311588 100755
--- a/run_in_compat_layer_env.sh
+++ b/run_in_compat_layer_env.sh
@@ -8,5 +8,11 @@ if [ ! -d ${EESSI_COMPAT_LAYER_DIR} ]; then
     echo "ERROR: ${EESSI_COMPAT_LAYER_DIR} does not exist!" >&2
     exit 1
 fi
-echo "Running '$@' in EESSI ${EESSI_PILOT_VERSION} compatibility layer environment..."
-${EESSI_COMPAT_LAYER_DIR}/startprefix <<< "$@"
+
+INPUT=$(echo "$@")
+if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
+    INPUT="export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}; ${INPUT}"
+fi
+
+echo "Running '${INPUT}' in EESSI ${EESSI_PILOT_VERSION} compatibility layer environment..."
+${EESSI_COMPAT_LAYER_DIR}/startprefix <<< "${INPUT}"