diff --git a/.docker/aiida-core-base/s6-assets/init/aiida-prepare.sh b/.docker/aiida-core-base/s6-assets/init/aiida-prepare.sh
index 690ebff536..a36783308e 100755
--- a/.docker/aiida-core-base/s6-assets/init/aiida-prepare.sh
+++ b/.docker/aiida-core-base/s6-assets/init/aiida-prepare.sh
@@ -5,34 +5,19 @@
 # Environment.
 export SHELL=/bin/bash
 
-# Configure AiiDA.
-export SETUP_DEFAULT_AIIDA_PROFILE=true
-export AIIDA_PROFILE_NAME=default
-export AIIDA_USER_EMAIL=aiida@localhost
-export AIIDA_USER_FIRST_NAME=Giuseppe
-export AIIDA_USER_LAST_NAME=Verdi
-export AIIDA_USER_INSTITUTION=Khedivial
-export AIIDA_PROFILE_PATH=/aiida/assets/config-quick-setup.yaml
-
 # Check if user requested to set up AiiDA profile (and if it exists already)
-if [[ ${SETUP_DEFAULT_AIIDA_PROFILE} == true ]] && ! verdi profile show ${AIIDA_PROFILE_NAME} &> /dev/null; then
-    NEED_SETUP_PROFILE=true;
-else
-    NEED_SETUP_PROFILE=false;
-fi
-
-# Setup AiiDA profile if needed.
-if [[ ${NEED_SETUP_PROFILE} == true ]]; then
+# If the environment variable `SETUP_DEFAULT_AIIDA_PROFILE` is not set, set it to `true`.
+if [[ ${SETUP_DEFAULT_AIIDA_PROFILE:-true} == true ]] && ! verdi profile show ${AIIDA_PROFILE_NAME} &> /dev/null; then
 
     # Create AiiDA profile.
     verdi quicksetup              \
         --non-interactive                            \
-        --profile "${AIIDA_PROFILE_NAME}"            \
-        --email "${AIIDA_USER_EMAIL}"                \
-        --first-name "${AIIDA_USER_FIRST_NAME}"      \
-        --last-name "${AIIDA_USER_LAST_NAME}"        \
-        --institution "${AIIDA_USER_INSTITUTION}"    \
-        --config "${AIIDA_PROFILE_PATH}"
+        --profile "${AIIDA_PROFILE_NAME:-default}"            \
+        --email "${AIIDA_USER_EMAIL:-aiida@localhost}"                \
+        --first-name "${AIIDA_USER_FIRST_NAME:-Giuseppe}"      \
+        --last-name "${AIIDA_USER_LAST_NAME:-Verdi}"        \
+        --institution "${AIIDA_USER_INSTITUTION:-Khedivial}"    \
+        --config "${AIIDA_CONFIG_FILE:-/aiida/assets/config-quick-setup.yaml}"
 
     # Supress verdi version warning because we are using a development version
     verdi config set warnings.development_version False
@@ -76,11 +61,11 @@ if [[ ${NEED_SETUP_PROFILE} == true ]]; then
     verdi computer configure core.local "${computer_name}" \
         --non-interactive                                               \
         --safe-interval 0.0
+
+    # Migration will run for the default profile.
+    verdi storage migrate --force
 fi
 
 
 # Show the default profile
 verdi profile show || echo "The default profile is not set."
-
-# Migration will run for the default profile.
-verdi storage migrate --force
diff --git a/docs/source/intro/run_docker.rst b/docs/source/intro/run_docker.rst
index e842d0cf28..5baa1b53b3 100644
--- a/docs/source/intro/run_docker.rst
+++ b/docs/source/intro/run_docker.rst
@@ -33,6 +33,22 @@ This image contains a fully pre-configured AiiDA environment which makes it part
 
          $ docker run -it --name aiida-container aiidateam/aiida-core-with-services:latest bash
 
+      By default, an AiiDA profile is automatically set up inside the container.
+      To disable this default profile being created, set the ``SETUP_DEFAULT_AIIDA_PROFILE`` environment variable to ``false``.
+
+      The following environment variables can be set to configure the default AiiDA profile:
+      - ``AIIDA_PROFILE_NAME``: the name of the profile to be created (default: ``default``)
+      - ``AIIDA_USER_EMAIL``: the email of the default user to be created (default: ``aiida@localhost``)
+      - ``AIIDA_USER_FIRST_NAME``: the first name of the default user to be created (default: ``Giuseppe``)
+      - ``AIIDA_USER_LAST_NAME``: the last name of the default user to be created (default: ``Verdi``)
+      - ``AIIDA_USER_INSTITUTION``: the institution of the default user to be created (default: ``Khedivial``)
+      - ``AIIDA_CONFIG_FILE``: the path to the AiiDA configuration file used for other profile configuration parameters (default: ``/aiida/assets/config-quick-setup.yaml``).
+
+      These environment variables can be set when starting the container with the ``-e`` option.
+
+      Please note that the ``AIIDA_CONFIG_FILE`` variable points to a path inside the container.
+      Therefore, if you want to use a custom configuration file, it needs to be mounted from the host path to the container path.
+
    .. grid-item-card:: Check setup
 
       The profile named ``default`` is created under the ``aiida`` user.