diff --git a/autoconf/Dockerfile b/autoconf/Dockerfile
index ecb595c..479f4a3 100644
--- a/autoconf/Dockerfile
+++ b/autoconf/Dockerfile
@@ -1,11 +1,15 @@
 FROM alpine
 
-RUN apk add py3-pip && \
-    pip3 install docker
+RUN apk add py3-pip apache2-utils bash && \
+    pip3 install docker && \
+    mkdir /opt/entrypoint && \
+    mkdir -p /opt/confs/site
 
-COPY *.py /opt/
-RUN chmod +x /opt/entrypoint.py
+COPY confs/site/ /opt/confs/site
+COPY entrypoint/* /opt/entrypoint/
+COPY autoconf/* /opt/entrypoint/
+RUN chmod +x /opt/entrypoint/*.py /opt/entrypoint/*.sh
 
 VOLUME /etc/nginx
 
-ENTRYPOINT ["/opt/entrypoint.py"]
+ENTRYPOINT ["/opt/entrypoint/entrypoint.py"]
diff --git a/autoconf/config.py b/autoconf/config.py
index 6314f89..68b73c3 100644
--- a/autoconf/config.py
+++ b/autoconf/config.py
@@ -1,13 +1,13 @@
 #!/usr/bin/python3
 
 import utils
-import subprocess, shutil, os
+import subprocess, shutil, os, traceback
 
 def generate(instances, vars) :
 	try :
 		# Get env vars from bunkerized-nginx instances
 		vars_instances = {}
-		for instance_id, instance in instances :
+		for instance_id, instance in instances.items() :
 			for var_value in instance.attrs["Config"]["Env"] :
 				var = var_value.split("=")[0]
 				value = var_value.replace(var + "=", "", 1)
@@ -16,10 +16,11 @@ def generate(instances, vars) :
 		vars_defaults.update(vars_instances)
 		vars_defaults.update(vars)
 		# Call site-config.sh to generate the config
-		proc = subprocess.run(["/opt/site-config.sh", vars["SERVER_NAME"]], env=vars_defaults, capture_output=True)
+		proc = subprocess.run(["/opt/entrypoint/site-config.sh", vars["SERVER_NAME"]], env=vars_defaults, capture_output=True)
 		if proc.returncode == 0 :
 			return True
 	except Exception as e :
+		traceback.print_exc()
 		utils.log("[!] Error while generating config : " + str(e))
 	return False
 
@@ -34,11 +35,11 @@ def activate(instances, vars) :
 		utils.replace_in_file("/etc/nginx/nginx.conf", "}", "include /etc/nginx/" + vars["SERVER_NAME"] + "/server.conf;\n}")
 
 		# Send SIGHUP to all running instances
-		for instance_id, instance in instances :
+		for instance_id, instance in instances.items() :
 			if instance.status == "running" :
 				try :
 					instance.kill("SIGHUP")
-					utils.log("[*] Sent SIGHUP signal to bunkerized-nginx instance " + instance.name + " / " + instance.id
+					utils.log("[*] Sent SIGHUP signal to bunkerized-nginx instance " + instance.name + " / " + instance.id)
 				except docker.errors.APIError as e :
 					utils.log("[!] Docker error while sending SIGHUP signal : " + str(e))
 		return True
@@ -57,11 +58,11 @@ def deactivate(instances, vars) :
 		utils.replace_in_file("/etc/nginx/nginx.conf", "include /etc/nginx/" + vars["SERVER_NAME"] + "/server.conf;\n", "")
 
 		# Send SIGHUP to all running instances
-		for instance_id, instance in instances :
+		for instance_id, instance in instances.items() :
 			if instance.status == "running" :
 				try :
 					instance.kill("SIGHUP")
-					utils.log("[*] Sent SIGHUP signal to bunkerized-nginx instance " + instance.name + " / " + instance.id
+					utils.log("[*] Sent SIGHUP signal to bunkerized-nginx instance " + instance.name + " / " + instance.id)
 				except docker.errors.APIError as e :
 					utils.log("[!] Docker error while sending SIGHUP signal : " + str(e))
 		return True
diff --git a/autoconf/entrypoint.py b/autoconf/entrypoint.py
index 2a601dc..d314966 100644
--- a/autoconf/entrypoint.py
+++ b/autoconf/entrypoint.py
@@ -32,23 +32,26 @@ def process(container, event) :
 			else :
 				utils.log("[!] Can't generate config for " + vars["SERVER_NAME"])
 		elif event == "start" :
-			containers[container.id].reload()
-			if config.activate(instances, vars) :
-				utils.log("[*] Activated config for " + vars["SERVER_NAME"])
-			else :
-				utils.log("[!] Can't activate config for " + vars["SERVER_NAME"])
+			if container.id in containers :
+				containers[container.id].reload()
+				if config.activate(instances, vars) :
+					utils.log("[*] Activated config for " + vars["SERVER_NAME"])
+				else :
+					utils.log("[!] Can't activate config for " + vars["SERVER_NAME"])
 		elif event == "die" :
-			containers[container.id].reload()
-			if config.deactivate(instances, vars) :
-				utils.log("[*] Deactivated config for " + vars["SERVER_NAME"])
-			else :
-				utils.log("[!] Can't deactivate config for " + vars["SERVER_NAME"])
+			if container.id in containers :
+				containers[container.id].reload()
+				if config.deactivate(instances, vars) :
+					utils.log("[*] Deactivated config for " + vars["SERVER_NAME"])
+				else :
+					utils.log("[!] Can't deactivate config for " + vars["SERVER_NAME"])
 		elif event == "destroy" :
-			del containers[container.id]
-			if config.remove(vars) :
-				utils.log("[*] Removed config for " + vars["SERVER_NAME"])
-			else :
-				utils.log("[!] Can't remove config for " + vars["SERVER_NAME"])
+			if container.id in containers :
+				del containers[container.id]
+				if config.remove(vars) :
+					utils.log("[*] Removed config for " + vars["SERVER_NAME"])
+				else :
+					utils.log("[!] Can't remove config for " + vars["SERVER_NAME"])
 
 # Connect to the endpoint
 endpoint = "/var/run/docker.sock"
diff --git a/confs/site/fastcgi.conf b/confs/site/fastcgi.conf
new file mode 100644
index 0000000..acd0b38
--- /dev/null
+++ b/confs/site/fastcgi.conf
@@ -0,0 +1,25 @@
+fastcgi_param  SCRIPT_FILENAME    $document_root$fastcgi_script_name;
+fastcgi_param  QUERY_STRING       $query_string;
+fastcgi_param  REQUEST_METHOD     $request_method;
+fastcgi_param  CONTENT_TYPE       $content_type;
+fastcgi_param  CONTENT_LENGTH     $content_length;
+
+fastcgi_param  SCRIPT_NAME        $fastcgi_script_name;
+fastcgi_param  REQUEST_URI        $request_uri;
+fastcgi_param  DOCUMENT_URI       $document_uri;
+fastcgi_param  DOCUMENT_ROOT      $document_root;
+fastcgi_param  SERVER_PROTOCOL    $server_protocol;
+fastcgi_param  REQUEST_SCHEME     $scheme;
+fastcgi_param  HTTPS              $https if_not_empty;
+
+fastcgi_param  GATEWAY_INTERFACE  CGI/1.1;
+fastcgi_param  SERVER_SOFTWARE    nginx/$nginx_version;
+
+fastcgi_param  REMOTE_ADDR        $remote_addr;
+fastcgi_param  REMOTE_PORT        $remote_port;
+fastcgi_param  SERVER_ADDR        $server_addr;
+fastcgi_param  SERVER_PORT        $server_port;
+fastcgi_param  SERVER_NAME        $server_name;
+
+# PHP only, required if PHP was built with --enable-force-cgi-redirect
+fastcgi_param  REDIRECT_STATUS    200;
diff --git a/entrypoint/entrypoint.sh b/entrypoint/entrypoint.sh
index 7e92fc0..61d63c0 100644
--- a/entrypoint/entrypoint.sh
+++ b/entrypoint/entrypoint.sh
@@ -30,6 +30,9 @@ trap "trap_exit" TERM INT
 # trap SIGHUP
 function trap_reload() {
 	echo "[*] Catched reload operation"
+	if [ "$MULTISITE" = "yes" ] ; then
+		/opt/entrypoint/multisite-config.sh
+	fi
 	if [ -f /tmp/nginx.pid ] ; then
 		echo "[*] Reloading nginx ..."
 		/usr/sbin/nginx -s reload
@@ -53,6 +56,7 @@ if [ ! -f "/opt/installed" ] ; then
 			/opt/entrypoint/site-config.sh "$server"
 			echo "[*] Multi site - $server configuration done"
 		done
+		/opt/entrypoint/multisite-config.sh
 	else
 		/opt/entrypoint/site-config.sh
 		echo "[*] Single site - $SERVER_NAME configuration done"
@@ -67,13 +71,6 @@ chown -R root:nginx /etc/nginx/
 chmod -R 740 /etc/nginx/
 find /etc/nginx -type d -exec chmod 750 {} \;
 
-# fix let's encrypt rights
-if [ "$AUTO_LETS_ENCRYPT" = "yes" ] ; then
-	chown -R root:nginx /etc/letsencrypt
-	chmod -R 740 /etc/letsencrypt
-	find /etc/letsencrypt -type d -exec chmod 750 {} \;
-fi
-
 # start rsyslogd
 rsyslogd
 
diff --git a/entrypoint/multisite-config.sh b/entrypoint/multisite-config.sh
new file mode 100644
index 0000000..6ac2c6a
--- /dev/null
+++ b/entrypoint/multisite-config.sh
@@ -0,0 +1,42 @@
+#!/bin/sh
+
+# load default values
+. /opt/entrypoint/defaults.sh
+
+# load some functions
+. /opt/entrypoint/utils.sh
+
+# fix nginx configs rights (and modules through the symlink)
+chown -R root:nginx /etc/nginx/
+chmod -R 740 /etc/nginx/
+find /etc/nginx -type d -exec chmod 750 {} \;
+
+if [ "$MULTISITE" = "yes" ] ; then
+	servers=$(find /etc/nginx -name "server.conf" | cut -d '/' -f 4)
+	for server in $servers ; do
+		SERVER_PREFIX="/etc/nginx/${server}/"
+		if grep "/etc/letsencrypt/live" ${SERVER_PREFIX}https.conf > /dev/null && [ ! -f /etc/letsencrypt/live/${server}/fullchain.pem ] ; then
+			/opt/scripts/certbot-new.sh "$1" "$(cat ${SERVER_PREFIX}email-lets-encrypt.txt)"
+		fi
+		if grep "modsecurity.conf" ${SERVER_PREFIX}server.conf > /dev/null ; then
+			modsec_custom=""
+			if ls /modsec-confs/*.conf > /dev/null 2>&1 ; then
+				modsec_custom="include /modsec-confs/*.conf\n"
+			fi
+			if ls /modsec-confs/${1}/*.conf > /dev/null 2>&1 ; then
+				modsec_custom="${modsec_custom}include /modsec-confs/${server}/*.conf\n"
+			fi
+			replace_in_file "${SERVER_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CUSTOM_RULES%" "$modsec_custom"
+			if grep "owasp-crs.conf" ${SERVER_PREFIX}modsecurity-rules.conf > /dev/null ; then
+				modsec_crs_custom=""
+				if ls /modsec-crs-confs/*.conf > /dev/null 2>&1 ; then
+					modsec_crs_custom="include /modsec-crs-confs/*.conf\n"
+				fi
+				if ls /modsec-crs-confs/${1}/*.conf > /dev/null 2>&1 ; then
+					modsec_crs_custom="${modsec_custom}include /modsec-crs-confs/${server}/*.conf\n"
+				fi
+			fi
+			replace_in_file "${SERVER_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CUSTOM_CRS%" "$modsec_crs_custom"
+		fi
+	done
+fi
diff --git a/entrypoint/site-config.sh b/entrypoint/site-config.sh
index d84e07e..4651952 100644
--- a/entrypoint/site-config.sh
+++ b/entrypoint/site-config.sh
@@ -137,9 +137,6 @@ if [ "$REMOTE_PHP" != "" ] ; then
 	replace_in_file "${NGINX_PREFIX}server.conf" "%USE_PHP%" "include ${NGINX_PREFIX}php.conf;"
 	replace_in_file "${NGINX_PREFIX}server.conf" "%FASTCGI_PATH%" "include ${NGINX_PREFIX}fastcgi.conf;"
 	replace_in_file "${NGINX_PREFIX}php.conf" "%REMOTE_PHP%" "$REMOTE_PHP"
-	if [ "$MULTISITE" = "yes" ] ; then
-		cp /etc/nginx/fastcgi.conf ${NGINX_PREFIX}fastcgi.conf && chown root:nginx ${NGINX_PREFIX}fastcgi.conf
-	fi
 	replace_in_file "${NGINX_PREFIX}fastcgi.conf" "\$document_root" "${REMOTE_PHP_PATH}/"
 else
 	replace_in_file "${NGINX_PREFIX}server.conf" "%USE_PHP%" ""
@@ -322,11 +319,8 @@ if [ "$AUTO_LETS_ENCRYPT" = "yes" ] || [ "$USE_CUSTOM_HTTPS" = "yes" ] || [ "$GE
 			FIRST_SERVER_NAME=$(echo "$SERVER_NAME" | cut -d " " -f 1)
 		else
 			FIRST_SERVER_NAME="$1"
-			if [ ! -f /etc/letsencrypt/live/${1}/fullchain.pem ] ; then
-				echo "[*] Performing Let's Encrypt challenge for $1 ..."
-				EMAIL_LETS_ENCRYPT="${EMAIL_LETS_ENCRYPT-contact@$1}"
-				/opt/scripts/certbot-new.sh "$1" "$EMAIL_LETS_ENCRYPT"
-			fi
+			EMAIL_LETS_ENCRYPT="${EMAIL_LETS_ENCRYPT-contact@$1}"
+			echo -n "$EMAIL_LETS_ENCRYPT" > ${NGINX_PREFIX}email-lets-encrypt.txt
 		fi
 		replace_in_file "${NGINX_PREFIX}https.conf" "%HTTPS_CERT%" "/etc/letsencrypt/live/${FIRST_SERVER_NAME}/fullchain.pem"
 		replace_in_file "${NGINX_PREFIX}https.conf" "%HTTPS_KEY%" "/etc/letsencrypt/live/${FIRST_SERVER_NAME}/privkey.pem"
@@ -362,24 +356,22 @@ fi
 if [ "$USE_MODSECURITY" = "yes" ] ; then
 	replace_in_file "${NGINX_PREFIX}modsecurity.conf" "%MODSEC_RULES_FILE%" "${NGINX_PREFIX}/modsecurity-rules.conf"
 	replace_in_file "${NGINX_PREFIX}server.conf" "%USE_MODSECURITY%" "include ${NGINX_PREFIX}modsecurity.conf;"
-	modsec_custom=""
-	if ls /modsec-confs/*.conf > /dev/null 2>&1 ; then
-		modsec_custom="include /modsec-confs/*.conf\n"
+	if [ "$MULTISITE" != "yes" ] ; then
+		modsec_custom=""
+		if ls /modsec-confs/*.conf > /dev/null 2>&1 ; then
+			modsec_custom="include /modsec-confs/*.conf\n"
+		fi
+		replace_in_file "${NGINX_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CUSTOM_RULES%" "$modsec_custom"
 	fi
-	if [ "$MULTISITE" = "yes" ] && ls /modsec-confs/${1}/*.conf > /dev/null 2>&1 ; then
-		modsec_custom="${modsec_custom}include /modsec-confs/${1}/*.conf\n"
-	fi
-	replace_in_file "${NGINX_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CUSTOM_RULES%" "$modsec_custom"
 	if [ "$USE_MODSECURITY_CRS" = "yes" ] ; then
 		replace_in_file "${NGINX_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CRS%" "include /etc/nginx/owasp-crs.conf"
-		modsec_crs_custom=""
-		if ls /modsec-crs-confs/*.conf > /dev/null 2>&1 ; then
-			modsec_crs_custom="include /modsec-crs-confs/*.conf\n"
+		if [ "$MULTISITE" != "yes" ] ; then
+			modsec_crs_custom=""
+			if ls /modsec-crs-confs/*.conf > /dev/null 2>&1 ; then
+				modsec_crs_custom="include /modsec-crs-confs/*.conf\n"
+			fi
+			replace_in_file "${NGINX_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CUSTOM_CRS%" "$modsec_crs_custom"
 		fi
-		if [ "$MULTISITE" = "yes" ] && ls /modsec-crs-confs/${1}/*.conf > /dev/null 2>&1 ; then
-			modsec_crs_custom="${modsec_custom}include /modsec-crs-confs/${1}/*.conf\n"
-		fi
-		replace_in_file "${NGINX_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CUSTOM_CRS%" "$modsec_crs_custom"
 		replace_in_file "${NGINX_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CRS_RULES%" "include /etc/nginx/owasp-crs/*.conf"
 	else
 		replace_in_file "${NGINX_PREFIX}modsecurity-rules.conf" "%MODSECURITY_INCLUDE_CRS%" ""
diff --git a/examples/autoconf-php/docker-compose.yml b/examples/autoconf-php/docker-compose.yml
index f8a56ba..38c0014 100644
--- a/examples/autoconf-php/docker-compose.yml
+++ b/examples/autoconf-php/docker-compose.yml
@@ -9,9 +9,9 @@ services:
       - 80:8080
       - 443:8443
     volumes:
-      - /var/run/docker.sock:/var/run/docker.sock:ro
       - ./letsencrypt:/etc/letsencrypt
       - ./web-files:/www:ro
+      - autoconf:/etc/nginx
     environment:
       - SERVER_NAME=                                   # must be left blank if you don't want to setup "static" conf
       - MULTISITE=yes
@@ -21,6 +21,15 @@ services:
       - USE_CLIENT_CACHE=yes
       - USE_GZIP=yes
       - USE_BROTLI=yes
+    labels:
+      - "bunkerized-nginx.AUTOCONF"
+
+  myautoconf:
+    image: bunkerity/bunkerized-nginx:autoconf
+    restart: always
+    volumes:
+      - /var/run/docker.sock:/var/run/docker.sock:ro
+      - autoconf:/etc/nginx
 
   myapp1:
     image: php:fpm
@@ -51,3 +60,6 @@ services:
       - "bunkerized-nginx.SERVER_NAME=app3.website.com" # replace with your domain
       - "bunkerized-nginx.REMOTE_PHP=myapp3"
       - "bunkerized-nginx.REMOTE_PHP_PATH=/app"
+
+volumes:
+  autoconf:
diff --git a/examples/autoconf-reverse-proxy/docker-compose.yml b/examples/autoconf-reverse-proxy/docker-compose.yml
index 0a8d731..daaa53b 100644
--- a/examples/autoconf-reverse-proxy/docker-compose.yml
+++ b/examples/autoconf-reverse-proxy/docker-compose.yml
@@ -9,8 +9,8 @@ services:
       - 80:8080
       - 443:8443
     volumes:
-      - /var/run/docker.sock:/var/run/docker.sock:ro
       - ./letsencrypt:/etc/letsencrypt
+      - autoconf:/etc/nginx
     environment:
       - SERVER_NAME=                                              # must be left blank if you don't want to setup "static" conf
       - MULTISITE=yes
@@ -22,6 +22,13 @@ services:
       - USE_BROTLI=yes
       - USE_REVERSE_PROXY=yes
 
+  myautoconf:
+    image: bunkerity/bunkerized-nginx:autoconf
+    restart: always
+    volumes:
+      - /var/run/docker.sock:/var/run/docker.sock:ro
+      - autoconf:/etc/nginx
+
   myapp1:
     build: js-app
     restart: always
@@ -51,3 +58,6 @@ services:
       - "bunkerized-nginx.SERVER_NAME=app3.website.com"            # replace with your domain
       - "bunkerized-nginx.REVERSE_PROXY_URL=/"
       - "bunkerized-nginx.REVERSE_PROXY_HOST=http://myapp3:3000"
+
+volumes:
+  autoconf: