diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index 7f04c50..03a5b61 100755
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -75,7 +75,7 @@ find ${GRAYLOG_HOME}/plugin ! -readable -prune -o -type f -a -readable -exec cp
 
 setup() {
   # Create data directories
-  for d in journal log plugin config contentpacks
+  for d in config contentpacks data journal scripts
   do
     dir=${GRAYLOG_HOME}/data/${d}
     [[ -d "${dir}" ]] || mkdir -p "${dir}"
@@ -109,15 +109,31 @@ setupCertificates() {
 }
 
 graylog() {
+  local log_config="${GRAYLOG_HOME}/config/log4j2.xml"
+  local graylog_config="${GRAYLOG_HOME}/config/graylog.conf"
+  local legacy_log_config="${GRAYLOG_HOME}/data/config/log4j2.xml"
+  local legacy_graylog_config="${GRAYLOG_HOME}/data/config/graylog.conf"
+
+  # Backward compatibility for setups that have existing (and potentially custom)
+  # logging and server configuration files in the data/config directory.
+  # See: https://github.com/Graylog2/docker-compose/issues/99
+  if [ -f "$legacy_log_config" ]; then
+    log_config="$legacy_log_config"
+    echo "WARNING: Using deprecated <$legacy_log_config> file. Switch to <$log_config>!"
+  fi
+  if [ -f "$legacy_graylog_config" ]; then
+    graylog_config="$legacy_graylog_config"
+    echo "WARNING: Using deprecated <$legacy_graylog_config> file. Switch to <$graylog_config>!"
+  fi
 
   exec "${JAVA_HOME}/bin/java" \
     ${GRAYLOG_SERVER_JAVA_OPTS} \
     -jar \
-    -Dlog4j.configurationFile="${GRAYLOG_HOME}/data/config/log4j2.xml" \
+    -Dlog4j.configurationFile="${log_config}" \
     -Dgraylog2.installation_source=docker \
     "${GRAYLOG_HOME}/graylog.jar" \
     "$@" \
-    -f "${GRAYLOG_HOME}/data/config/graylog.conf"
+    -f "${graylog_config}"
 }
 
 run() {
diff --git a/docker/enterprise/Dockerfile b/docker/enterprise/Dockerfile
index 7a9c42c..0c30135 100644
--- a/docker/enterprise/Dockerfile
+++ b/docker/enterprise/Dockerfile
@@ -80,13 +80,15 @@ RUN \
     /opt/graylog/data/data \
     /opt/graylog/data/scripts
 
+# hadolint ignore=DL3059
+RUN install --directory --mode=0750 /opt/graylog/config
 
 RUN mv /opt/graylog ${GRAYLOG_HOME} && chown -R ${GRAYLOG_UID}:${GRAYLOG_GID} ${GRAYLOG_HOME}
 RUN mv ${GRAYLOG_HOME}/plugin ${GRAYLOG_HOME}/plugins-default
 RUN install -d -o "${GRAYLOG_UID}" -g "${GRAYLOG_GID}" -m 0755 ${GRAYLOG_HOME}/plugins-merged && \
     install -d -o "${GRAYLOG_UID}" -g "${GRAYLOG_GID}" -m 0755 ${GRAYLOG_HOME}/plugin
 
-COPY config ${GRAYLOG_HOME}/data/config
+COPY config ${GRAYLOG_HOME}/config
 
 # -------------------------------------------------------------------------------------------------
 #
diff --git a/docker/oss/Dockerfile b/docker/oss/Dockerfile
index d59f58e..fe3683a 100644
--- a/docker/oss/Dockerfile
+++ b/docker/oss/Dockerfile
@@ -68,12 +68,15 @@ RUN \
     /opt/graylog/data/plugin \
     /opt/graylog/data/data
 
+# hadolint ignore=DL3059
+RUN install --directory --mode=0750 /opt/graylog/config
+
 RUN mv /opt/graylog ${GRAYLOG_HOME} && chown -R ${GRAYLOG_UID}:${GRAYLOG_GID} ${GRAYLOG_HOME}
 RUN mv ${GRAYLOG_HOME}/plugin ${GRAYLOG_HOME}/plugins-default
 RUN install -d -o "${GRAYLOG_UID}" -g "${GRAYLOG_GID}" -m 0755 ${GRAYLOG_HOME}/plugins-merged && \
     install -d -o "${GRAYLOG_UID}" -g "${GRAYLOG_GID}" -m 0755 ${GRAYLOG_HOME}/plugin
 
-COPY config ${GRAYLOG_HOME}/data/config
+COPY config ${GRAYLOG_HOME}/config
 
 # -------------------------------------------------------------------------------------------------
 #
diff --git a/health_check.sh b/health_check.sh
index 74ba4ce..27fc528 100755
--- a/health_check.sh
+++ b/health_check.sh
@@ -14,13 +14,23 @@ source /etc/profile
 proto=http
 http_bind_address=127.0.0.1:9000
 
+graylog_config="${GRAYLOG_HOME}/config/graylog.conf"
+legacy_graylog_config="${GRAYLOG_HOME}/data/config/graylog.conf"
+
+# Backward compatibility for setups that have an existing (and potentially custom)
+# server configuration file in the data/config directory.
+# See: https://github.com/Graylog2/docker-compose/issues/99
+if [[ -f "$legacy_graylog_config" ]]; then
+	graylog_config="$legacy_graylog_config"
+fi
+
 # check if configuration file is given and grep for variable
-if [[ -f "${GRAYLOG_HOME}"/data/config/graylog.conf ]]
+if [[ -f "$graylog_config" ]]
 then
 	# try to grep the variable from a mounted configuration
-	http_publish_uri=$(grep "^http_publish_uri" "${GRAYLOG_HOME}"/data/config/graylog.conf | awk -F '=' '{print $2}' | awk '{$1=$1};1')
-	http_bind_address=$(grep "^http_bind_address" "${GRAYLOG_HOME}"/data/config/graylog.conf | awk -F '=' '{print $2}' | awk '{$1=$1};1')
-	http_enable_tls=$(grep "^http_enable_tls" "${GRAYLOG_HOME}"/data/config/graylog.conf | awk -F '=' '{print $2}' | awk '{$1=$1};1')
+	http_publish_uri=$(grep "^http_publish_uri" "$graylog_config" | awk -F '=' '{print $2}' | awk '{$1=$1};1')
+	http_bind_address=$(grep "^http_bind_address" "$graylog_config" | awk -F '=' '{print $2}' | awk '{$1=$1};1')
+	http_enable_tls=$(grep "^http_enable_tls" "$graylog_config" | awk -F '=' '{print $2}' | awk '{$1=$1};1')
 
 	# FIX https://github.com/Graylog2/graylog-docker/issues/102
 	# This will remove the protocol from the URI if set via