diff --git a/batch/hpc_init.sh b/batch/hpc_init.sh
index 71091f580..c90134a60 100644
--- a/batch/hpc_init.sh
+++ b/batch/hpc_init.sh
@@ -52,6 +52,7 @@ if [ -z "${FLEPI_CONDA}" ]; then
     fi
     echo "Using '$FLEPI_CONDA' for \$FLEPI_CONDA."
 fi
+conda deactivate
 conda activate $FLEPI_CONDA
 
 # Check the conda environment is valid