diff --git a/wazuh/Dockerfile b/wazuh/Dockerfile
index 04b05d90..92dad7c0 100644
--- a/wazuh/Dockerfile
+++ b/wazuh/Dockerfile
@@ -41,20 +41,19 @@ COPY config/filebeat.yml /etc/filebeat/
 
 RUN chmod go-w /etc/filebeat/filebeat.yml
 
+ADD https://raw.githubusercontent.com/wazuh/wazuh/$TEMPLATE_VERSION/extensions/elasticsearch/7.x/wazuh-template.json /etc/filebeat
+RUN chmod go-w /etc/filebeat/wazuh-template.json
+
 COPY config/etc/ /etc/
 
-COPY config/data_dirs.env /
-
-# Setting volumes
-VOLUME ["/var/ossec/data"]
-VOLUME ["/etc/filebeat"]
-VOLUME ["/var/lib/filebeat"]
+# Prepare permanent data
+# Sync calls are due to https://github.com/docker/docker/issues/9547
+COPY config/permanent_data.env config/permanent_data.sh /
+RUN chmod 755 /permanent_data.sh && \
+    sync && /permanent_data.sh && \
+    sync && rm /permanent_data.sh
 
 # Services ports
 EXPOSE 55000/tcp 1514/udp 1515/tcp 514/udp 1516/tcp
 
-
-ADD https://raw.githubusercontent.com/wazuh/wazuh/$TEMPLATE_VERSION/extensions/elasticsearch/7.x/wazuh-template.json /etc/filebeat
-RUN chmod go-w /etc/filebeat/wazuh-template.json 
-
 ENTRYPOINT [ "/init" ]
diff --git a/wazuh/config/etc/cont-init.d/0-wazuh-init b/wazuh/config/etc/cont-init.d/0-wazuh-init
index 10796414..2fb840dd 100644
--- a/wazuh/config/etc/cont-init.d/0-wazuh-init
+++ b/wazuh/config/etc/cont-init.d/0-wazuh-init
@@ -4,14 +4,18 @@
 # Wazuh container bootstrap. See the README for information of the environment
 # variables expected by this script.
 
-# Startup the services
-
-FIRST_TIME_INSTALLATION=true
+# Variables
+source /permanent_data.env
 
 WAZUH_INSTALL_PATH=/var/ossec
-DATA_PATH=${WAZUH_INSTALL_PATH}/data
-
 WAZUH_CONFIG_MOUNT=/wazuh-config-mount
+AUTO_ENROLLMENT_ENABLED=${AUTO_ENROLLMENT_ENABLED:-true}
+API_GENERATE_CERTS=${API_GENERATE_CERTS:-true}
+
+
+##############################################################################
+# Aux functions
+##############################################################################
 
 print() {
     echo -e $1
@@ -31,72 +35,219 @@ exec_cmd_stdout() {
     eval $1 2>&1 || error_and_exit "$1"
 }
 
+##############################################################################
+# Edit configuration
+##############################################################################
+
 edit_configuration() { # $1 -> setting,  $2 -> value
     sed -i "s/^config.$1\s=.*/config.$1 = \"$2\";/g" "${DATA_PATH}/api/configuration/config.js" || error_and_exit "sed (editing configuration)"
 }
 
-if [  -e ${WAZUH_INSTALL_PATH}/etc-template  ]
-then
-    cp -p /var/ossec/etc-template/internal_options.conf /var/ossec/etc/internal_options.conf
-fi
-rm /var/ossec/queue/db/.template.db
+##############################################################################
+# This function will attempt to mount every directory in PERMANENT_DATA 
+# into the respective path. 
+# If the path is empty means permanent data volume is also empty, so a backup  
+# will be copied into it. Otherwise it will not be copied because there is  
+# already data inside the volume for the specified path.
+##############################################################################
 
-touch ${DATA_PATH}/process_list
-chgrp ossec ${DATA_PATH}/process_list
-chmod g+rw ${DATA_PATH}/process_list
-
-AUTO_ENROLLMENT_ENABLED=${AUTO_ENROLLMENT_ENABLED:-true}
-API_GENERATE_CERTS=${API_GENERATE_CERTS:-true}
+mount_permanent_data() {
+  for permanent_dir in "${PERMANENT_DATA[@]}"; do
+    # Check if the path is not empty
+    if find ${permanent_dir} -mindepth 1 | read; then
+      print "The path ${permanent_dir} is already mounted"
+    else
+      print "Installing ${permanent_dir}"
+      exec_cmd "cp -a ${WAZUH_INSTALL_PATH}/data_tmp/permanent${permanent_dir}/. ${permanent_dir}"
+    fi
+  done
+}
 
 ##############################################################################
-# Copy all files from $WAZUH_CONFIG_MOUNT to $DATA_PATH and respect
+# This function will replace from the permanent data volume every file 
+# contained in PERMANENT_DATA_EXCP
+# Some files as 'internal_options.conf' are saved as permanent data, but 
+# they must be updated to work properly if wazuh version is changed.
+##############################################################################
+
+apply_exclusion_data() {
+  for exclusion_file in "${PERMANENT_DATA_EXCP[@]}"; do
+    if [  -e ${WAZUH_INSTALL_PATH}/data_tmp/exclusion/${exclusion_file}  ]
+    then
+      DIR=$(dirname "${exclusion_file}")
+      if [ ! -e ${DIR}  ]
+      then
+        mkdir -p ${DIR}
+      fi
+      
+      print "Updating ${exclusion_file}"
+      exec_cmd "cp -p ${WAZUH_INSTALL_PATH}/data_tmp/exclusion/${exclusion_file} ${exclusion_file}"
+    fi
+  done
+}
+
+##############################################################################
+# This function will delete from the permanent data volume every file 
+# contained in PERMANENT_DATA_DEL
+##############################################################################
+
+remove_data_files() {
+  for del_file in "${PERMANENT_DATA_DEL[@]}"; do
+    if [ -e ${del_file} ]
+    then 
+      print "Removing ${del_file}"
+      exec_cmd "rm ${del_file}"
+    fi
+  done
+}
+
+##############################################################################
+# Create certificates: Manager
+##############################################################################
+
+create_ossec_key_cert() {
+  print "Creating ossec-authd key and cert"
+  exec_cmd "openssl genrsa -out ${WAZUH_INSTALL_PATH}/etc/sslmanager.key 4096"
+  exec_cmd "openssl req -new -x509 -key ${WAZUH_INSTALL_PATH}/etc/sslmanager.key -out ${WAZUH_INSTALL_PATH}/etc/sslmanager.cert -days 3650 -subj /CN=${HOSTNAME}/"
+}
+
+##############################################################################
+# Create certificates: API
+##############################################################################
+
+create_api_key_cert() {
+  print "Enabling Wazuh API HTTPS"
+  edit_configuration "https" "yes"
+  print "Create Wazuh API key and cert"
+  exec_cmd "openssl genrsa -out ${WAZUH_INSTALL_PATH}/api/configuration/ssl/server.key 4096"
+  exec_cmd "openssl req -new -x509 -key ${WAZUH_INSTALL_PATH}/api/configuration/ssl/server.key -out ${WAZUH_INSTALL_PATH}/api/configuration/ssl/server.crt -days 3650 -subj /CN=${HOSTNAME}/"
+
+  # Granting proper permissions 
+  chmod 400 ${WAZUH_INSTALL_PATH}/api/configuration/ssl/server.key
+  chmod 400 ${WAZUH_INSTALL_PATH}/api/configuration/ssl/server.crt
+}
+
+##############################################################################
+# Copy all files from $WAZUH_CONFIG_MOUNT to $WAZUH_INSTALL_PATH and respect
 # destination files permissions
 #
 # For example, to mount the file /var/ossec/data/etc/ossec.conf, mount it at
 # $WAZUH_CONFIG_MOUNT/etc/ossec.conf in your container and this code will
 # replace the ossec.conf file in /var/ossec/data/etc with yours.
 ##############################################################################
-if [ -e "$WAZUH_CONFIG_MOUNT" ]
-then
-  print "Identified Wazuh configuration files to mount..."
 
-  exec_cmd_stdout "cp --verbose -r $WAZUH_CONFIG_MOUNT/* $DATA_PATH"
-else
-  print "No Wazuh configuration files to mount..."
-fi
+mount_files() {
+  if [ -e "$WAZUH_CONFIG_MOUNT" ]
+  then
+    print "Identified Wazuh configuration files to mount..."
+    exec_cmd_stdout "cp --verbose -r $WAZUH_CONFIG_MOUNT/* $WAZUH_INSTALL_PATH"
+  else
+    print "No Wazuh configuration files to mount..."
+  fi
+}
+
+
+##############################################################################
+# Stop OSSEC
+##############################################################################
 
 function ossec_shutdown(){
   ${WAZUH_INSTALL_PATH}/bin/ossec-control stop;
 }
 
-# Trap exit signals and do a proper shutdown
-trap "ossec_shutdown; exit" SIGINT SIGTERM
-
-chmod -R g+rw ${DATA_PATH}
-
 ##############################################################################
 # Interpret any passed arguments (via docker command to this entrypoint) as
-# paths or commands, and execute them.
+# paths or commands, and execute them. 
 #
 # This can be useful for actions that need to be run before the services are
 # started, such as "/var/ossec/bin/ossec-control enable agentless".
 ##############################################################################
-for CUSTOM_COMMAND in "$@"
-do
-  echo "Executing command \`${CUSTOM_COMMAND}\`"
-  exec_cmd_stdout "${CUSTOM_COMMAND}"
-done
+
+docker_custom_args() {
+  for CUSTOM_COMMAND in "$@"
+  do
+    echo "Executing command \`${CUSTOM_COMMAND}\`"
+    exec_cmd_stdout "${CUSTOM_COMMAND}"
+  done
+}
 
 ##############################################################################
 # Change Wazuh API user credentials.
 ##############################################################################
 
-pushd /var/ossec/api/configuration/auth/
+change_api_user_credentials() {
+  pushd /var/ossec/api/configuration/auth/
+  if [[ "x${SECURITY_CREDENTIALS_FILE}" == "x" ]]; then
+    WAZUH_API_USER=${API_USER}
+    WAZUH_API_PASS=${API_PASS}
+  else
+    input=${SECURITY_CREDENTIALS_FILE}
+    while IFS= read -r line
+    do
+      if [[ $line == *"WAZUH_API_USER"* ]]; then
+        arrIN=(${line//:/ })
+        WAZUH_API_USER=${arrIN[1]}
+      elif [[ $line == *"WAZUH_API_PASS"* ]]; then
+        arrIN=(${line//:/ })
+        WAZUH_API_PASS=${arrIN[1]}
+      fi
+    done < "$input"
+  fi
 
-env
+  echo "Change Wazuh API user credentials"
+  change_user="node htpasswd -b -c user $WAZUH_API_USER $WAZUH_API_PASS"
+  eval $change_user
+  popd
+}
 
-echo "Change Wazuh API user credentials"
-change_user="node htpasswd -b -c user $API_USER $API_PASS"
-eval $change_user
 
-popd
+##############################################################################
+# Main function
+##############################################################################
+
+main() {
+  # Mount permanent data  (i.e. ossec.conf)
+  mount_permanent_data
+
+  # Restore files stored in permanent data that are not permanent  (i.e. internal_options.conf)
+  apply_exclusion_data
+
+  # Remove some files in permanent_data (i.e. .template.db)
+  remove_data_files
+
+  # Generate ossec-authd certs if AUTO_ENROLLMENT_ENABLED is true and does not exist
+  if [ $AUTO_ENROLLMENT_ENABLED == true ]
+  then
+    if [ ! -e ${WAZUH_INSTALL_PATH}/etc/sslmanager.key ]
+    then
+      create_ossec_key_cert
+    fi
+  fi
+
+  # Generate API certs if API_GENERATE_CERTS is true and does not exist
+  if [ $API_GENERATE_CERTS == true ]
+  then
+    if [ ! -e ${WAZUH_INSTALL_PATH}/api/configuration/ssl/server.crt ]
+    then
+      create_api_key_cert
+    fi
+  fi
+
+  # Mount selected files (WAZUH_CONFIG_MOUNT) to container
+  mount_files
+
+  # Trap exit signals and do a proper shutdown
+  trap "ossec_shutdown; exit" SIGINT SIGTERM
+
+  # Execute custom args
+  docker_custom_args
+
+  # Change API user credentials
+  change_api_user_credentials
+
+  # Delete temporary data folder
+  rm -rf ${WAZUH_INSTALL_PATH}/data_tmp
+
+}
+
+main
diff --git a/wazuh/config/init.bash b/wazuh/config/init.bash
deleted file mode 100644
index e40fab94..00000000
--- a/wazuh/config/init.bash
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-# Wazuh Docker Copyright (C) 2019 Wazuh Inc. (License GPLv2)
-
-# Initialize the custom data directory layout
-source /data_dirs.env
-
-cd /var/ossec
-for ossecdir in "${DATA_DIRS[@]}"; do
-  mv ${ossecdir} ${ossecdir}-template
-  ln -s $(realpath --relative-to=$(dirname ${ossecdir}) data)/${ossecdir} ${ossecdir}
-done
diff --git a/wazuh/config/permanent_data.env b/wazuh/config/permanent_data.env
new file mode 100644
index 00000000..b19409ac
--- /dev/null
+++ b/wazuh/config/permanent_data.env
@@ -0,0 +1,61 @@
+# Permanent data mounted in volumes
+i=0
+PERMANENT_DATA[((i++))]="/var/ossec/api/configuration"
+PERMANENT_DATA[((i++))]="/var/ossec/etc"
+PERMANENT_DATA[((i++))]="/var/ossec/logs"
+PERMANENT_DATA[((i++))]="/var/ossec/queue"
+PERMANENT_DATA[((i++))]="/var/ossec/var/multigroups"
+PERMANENT_DATA[((i++))]="/var/ossec/integrations"
+PERMANENT_DATA[((i++))]="/var/ossec/active-response/bin"
+PERMANENT_DATA[((i++))]="/var/ossec/wodles"
+PERMANENT_DATA[((i++))]="/etc/filebeat"
+export PERMANENT_DATA
+
+# Files mounted in a volume that should not be permanent
+i=0
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/etc/internal_options.conf"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/integrations/pagerduty"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/integrations/slack"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/integrations/slack.py"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/integrations/virustotal"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/integrations/virustotal.py"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/default-firewall-drop.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/disable-account.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/firewalld-drop.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/firewall-drop.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/host-deny.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/ip-customblock.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/ipfw_mac.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/ipfw.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/kaspersky.py"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/kaspersky.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/npf.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/ossec-slack.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/ossec-tweeter.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/pf.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/restart-ossec.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/restart.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/active-response/bin/route-null.sh"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/aws/aws-s3"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/aws/aws-s3.py"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/azure/azure-logs"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/azure/azure-logs.py"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/docker/DockerListener"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/docker/DockerListener.py"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/oscap"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/oscap.py"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/template_oval.xsl"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/template_xccdf.xsl"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/content/cve-redhat-6-ds.xml"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/content/cve-redhat-7-ds.xml"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/content/ssg-centos-6-ds.xml"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/content/ssg-centos-7-ds.xml"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/content/ssg-fedora-24-ds.xml"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/content/ssg-rhel-6-ds.xml"
+PERMANENT_DATA_EXCP[((i++))]="/var/ossec/wodles/oscap/content/ssg-rhel-7-ds.xml"
+export PERMANENT_DATA_EXCP
+
+# Files mounted in a volume that should be deleted 
+i=0
+PERMANENT_DATA_DEL[((i++))]="/var/ossec/queue/db/.template.db"
+export PERMANENT_DATA_DEL
diff --git a/wazuh/config/permanent_data.sh b/wazuh/config/permanent_data.sh
new file mode 100644
index 00000000..7a9d55b4
--- /dev/null
+++ b/wazuh/config/permanent_data.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+# Wazuh App Copyright (C) 2019 Wazuh Inc. (License GPLv2)
+
+# Variables
+source /permanent_data.env
+
+WAZUH_INSTALL_PATH=/var/ossec
+DATA_TMP_PATH=${WAZUH_INSTALL_PATH}/data_tmp
+mkdir ${DATA_TMP_PATH}
+
+# Move exclusion files to EXCLUSION_PATH
+EXCLUSION_PATH=${DATA_TMP_PATH}/exclusion
+mkdir ${EXCLUSION_PATH}
+
+for exclusion_file in "${PERMANENT_DATA_EXCP[@]}"; do
+  # Create the directory for the exclusion file if it does not exist
+  DIR=$(dirname "${exclusion_file}")
+  if [ ! -e ${EXCLUSION_PATH}/${DIR}  ]
+  then
+    mkdir -p ${EXCLUSION_PATH}/${DIR}
+  fi
+
+  mv ${exclusion_file} ${EXCLUSION_PATH}/${exclusion_file}
+done
+
+# Move permanent files to PERMANENT_PATH
+PERMANENT_PATH=${DATA_TMP_PATH}/permanent
+mkdir ${PERMANENT_PATH}
+
+for permanent_dir in "${PERMANENT_DATA[@]}"; do
+  # Create the directory for the permanent file if it does not exist
+  DIR=$(dirname "${permanent_dir}")
+  if [ ! -e ${PERMANENT_PATH}${DIR}  ]
+  then
+    mkdir -p ${PERMANENT_PATH}${DIR}
+  fi
+  
+  mv ${permanent_dir} ${PERMANENT_PATH}${permanent_dir}
+
+done
\ No newline at end of file