diff --git a/README.md b/README.md
index 8e7bfce..46a8786 100644
--- a/README.md
+++ b/README.md
@@ -49,9 +49,9 @@ Your tomcat server must be configured to
  * respond with HTTP return code less than 400, on `http://localhost:${LOCAL_HTTP_PORT}/` (default port 8080).
 
 If successful, the certificate files will be stored here:
-  * Certificate file: `/certs/${DOMAIN}/cert.pem`
-  * Certificate private key file: `/certs/${DOMAIN}/privkey.pem`
-  * Certificate chain file: `/certs/${DOMAIN}/fullchain.pem`
+  * Certificate file: `${CERT_DIR}/${DOMAIN}/cert.pem`
+  * Certificate private key file: `${CERT_DIR}/${DOMAIN}/privkey.pem`
+  * Certificate chain file: `${CERT_DIR}/${DOMAIN}/fullchain.pem`
 
 # Configuration at runtime
 
@@ -63,8 +63,20 @@ If successful, the certificate files will be stored here:
   * `ENABLE_LETSENCRYPT` - if set to `false` the letsencrypt process is not started 
   * `CREATE_SELFSIGNED` - if set to `false` no selfsigned certifcate is generated at start up.  
      Depending on your setup this might result in failing startup of the tomcat connectors
-* Persistence: Your certs are stored inside your container at `CERT_DIR` (default: `/certs/`), so you might want to 
-  persist this folder.
+  * `DEHYDRATED_BASEDIR` - defaults to `/dehydrated` for compatibility with letsencrypt-tomcat <= 0.40.
+  * `CERT_DIR` - if `DEHYDRATED_BASEDIR` is set, defaults to `$DEHYDRATED_BASEDIR/certs`, which is the default of dehydrated. If `DEHYDRATED_BASEDIR` is not set, defaults to `/certs` to be compatible with older letsencrypt-tomcat releases <=0.4.0.
+  * `DEHYDRATED_WELLKNOWN` - path where dehydrated will place ACME challenge files. Should usually be the document root of a webserver with `/.well-known/acme-challenge` appended.
+
+Note: if you want to save certificates and accounts in persistent storage it is highly recommended to set `DEHYDRATED_BASEDIR` env variable as described below.
+
+`DEHYDRATED_BASEDIR` and `CERT_DIR` interact:
+  * default (<=0.4.0) if `DEHYDRATED_BASEDIR` is not set:
+    * `DEHYDRATED_BASEDIR="/dehydrated" CERT_DIR="/certs"`
+    * `/dehydrated` is not stored in persistent storage and will be deleted with the container (including the letsencrypt account)
+  * recommended (>0.4.0):
+    * set `DEHYDRATED_BASEDIR="/certs/dehydrated"`. This will set `CERT_DIR="$DEHYDRATED_BASEDIR/certs"`. This allows all the certificates and dehydrated state (most importantly, accounts) to be stored in one directory, usually a volume mounted at `/certs`.
+
+It is possible to set environment variables in any place Docker supports, and will make them set in the container. This is: in a Dockerfile, as run parameters, as docker-compose.yml configuration, or in an .env file.
 
 # Run Examples
 
@@ -94,4 +106,4 @@ docker build -t schnatterer/letsencrypt-tomcat .
 docker build -t schnatterer/letsencrypt-tomcat:standalone --file=examples/standalone/Dockerfile .
 docker build -t schnatterer/letsencrypt-tomcat:spring-boot --file=examples/spring-boot/Dockerfile .
 docker build -t schnatterer/letsencrypt-tomcat:embedded-tomcat --file=examples/embedded-tomcat/Dockerfile .
-```
\ No newline at end of file
+```
diff --git a/etc/dehydrated/config b/etc/dehydrated/config
index 8a2121c..84cc44c 100644
--- a/etc/dehydrated/config
+++ b/etc/dehydrated/config
@@ -1,4 +1,5 @@
 # See https://github.com/dehydrated-io/dehydrated/blob/master/docs/examples/config
 
-WELLKNOWN="/static/.well-known/acme-challenge"
-BASEDIR="/dehydrated"
+WELLKNOWN="$DEHYDRATED_WELLKNOWN"
+BASEDIR="$DEHYDRATED_BASEDIR"
+CERTDIR="$CERT_DIR"
diff --git a/examples/embedded-tomcat/Dockerfile b/examples/embedded-tomcat/Dockerfile
index 5184532..2af80ed 100644
--- a/examples/embedded-tomcat/Dockerfile
+++ b/examples/embedded-tomcat/Dockerfile
@@ -21,6 +21,7 @@ RUN mvn package
 FROM letsencrypt-tomcat as aggregator
 # Copy letsencrypt-related stuff
 RUN mv /letsencrypt /dist
+ENV DEHYDRATED_BASEDIR="/certs/dehydrated"
 
 # Copy Libraries: Apache Portable Runtime (APR) and JNI wrappers for APR used by Tomcat (libtcnative)
 RUN cp -r /lib/* /dist/
diff --git a/examples/embedded-tomcat/src/main/java/info/schnatterer/tomcat/Main.java b/examples/embedded-tomcat/src/main/java/info/schnatterer/tomcat/Main.java
index 7148497..0affa61 100644
--- a/examples/embedded-tomcat/src/main/java/info/schnatterer/tomcat/Main.java
+++ b/examples/embedded-tomcat/src/main/java/info/schnatterer/tomcat/Main.java
@@ -15,7 +15,7 @@ public class Main {
 
     private static final int HTTPS_PORT = 8443;
     public static final String DOMAIN = System.getenv("DOMAIN");
-    public static final String CERT_FOLDER = "/certs/";
+    public static final String CERT_FOLDER = System.getenv("CERT_DIR");
     public static final String PK = CERT_FOLDER + DOMAIN + "/privkey.pem";
     public static final String CRT = CERT_FOLDER + DOMAIN + "/cert.pem";
     public static final String CA = CERT_FOLDER + DOMAIN + "/fullchain.pem";
diff --git a/examples/spring-boot/Dockerfile b/examples/spring-boot/Dockerfile
index 51a6298..64ef303 100644
--- a/examples/spring-boot/Dockerfile
+++ b/examples/spring-boot/Dockerfile
@@ -21,6 +21,7 @@ RUN mvn package
 FROM letsencrypt-tomcat as aggregator
 # Copy letsencrypt-related stuff
 RUN mv /letsencrypt /dist
+ENV DEHYDRATED_BASEDIR="/certs/dehydrated"
 
 # Copy Libraries: Apache Portable Runtime (APR) and JNI wrappers for APR used by Tomcat (libtcnative)
 RUN cp -r /lib/* /dist/
diff --git a/examples/spring-boot/src/main/resources/application.properties b/examples/spring-boot/src/main/resources/application.properties
index e14803b..4cfb082 100644
--- a/examples/spring-boot/src/main/resources/application.properties
+++ b/examples/spring-boot/src/main/resources/application.properties
@@ -4,6 +4,6 @@ server.http.port=8080
 # Needed so the letsencrypt challenge is served by tomcat
 spring.resources.staticLocations=file:/static
 
-server.ssl.certificateKeyFile=/certs/${DOMAIN}/privkey.pem
-server.ssl.certificateFile=/certs/${DOMAIN}/cert.pem
-server.ssl.certificateChainFile=/certs/${DOMAIN}/fullchain.pem
\ No newline at end of file
+server.ssl.certificateKeyFile=${certdir}/${DOMAIN}/privkey.pem
+server.ssl.certificateFile=${certdir}/${DOMAIN}/cert.pem
+server.ssl.certificateChainFile=${certdir}/${DOMAIN}/fullchain.pem
diff --git a/examples/standalone/Dockerfile b/examples/standalone/Dockerfile
index 4621005..076a664 100644
--- a/examples/standalone/Dockerfile
+++ b/examples/standalone/Dockerfile
@@ -7,17 +7,14 @@ FROM schnatterer/letsencrypt-tomcat:${LETSENCRYPT_TOMCAT_VERSION} as letsencrypt
 FROM letsencrypt-tomcat as aggregator
 # Copy letsencrypt-related stuff
 RUN mv /letsencrypt /dist
+ENV DEHYDRATED_BASEDIR="/certs/dehydrated"
 
 # Copy reloding connector, so tomcat can automatically reload certificates at runtime
 RUN mkdir -p /dist/opt/bitnami/tomcat/lib/
 RUN cp -r /tomcat-reloading-connector/* /dist/opt/bitnami/tomcat/lib/
 
-# Make standalone tomcat serve static files in directories used for letsencrypt challenges
-RUN mkdir -p /dist/opt/bitnami/tomcat/webapps/ROOT/.well-known/acme-challenge
-# It would be simpler to link ROOT -> static but it seems that tomcat does not follow symlinks when serving static content
-# So just do it the other way round
-RUN rm -rf /dist/static/.well-known/acme-challenge
-RUN ln -s /opt/bitnami/tomcat/webapps/ROOT/.well-known/acme-challenge /dist/static/.well-known/acme-challenge
+# set directory where dehydrated will create ACME challenge files
+ENV DEHYDRATED_WELLKNOWN="/opt/bitnami/tomcat/webapps/ROOT/.well-known/acme-challenge"
 
 # Copy examples/standalone tomcat config
 COPY examples/standalone/tomcat /dist/opt/bitnami/tomcat/
@@ -31,4 +28,4 @@ FROM tomcat
 VOLUME /certs/
 COPY --from=aggregator --chown=1001:0 /dist /
 ENTRYPOINT [ "/meta-entrypoint.sh", "/opt/bitnami/scripts/tomcat/entrypoint.sh" ]
-CMD [ "/opt/bitnami/scripts/tomcat/run.sh" ]
\ No newline at end of file
+CMD [ "/opt/bitnami/scripts/tomcat/run.sh" ]
diff --git a/examples/standalone/tomcat/conf/server.xml b/examples/standalone/tomcat/conf/server.xml
index e47a6d6..d9fa724 100644
--- a/examples/standalone/tomcat/conf/server.xml
+++ b/examples/standalone/tomcat/conf/server.xml
@@ -103,9 +103,9 @@
                maxThreads="150" SSLEnabled="true" >
         <UpgradeProtocol className="org.apache.coyote.http2.Http2Protocol" />
         <SSLHostConfig>
-            <Certificate certificateKeyFile="/certs/${domain}/privkey.pem"
-                         certificateFile="/certs/${domain}/cert.pem"
-                         certificateChainFile="/certs/${domain}/fullchain.pem"
+            <Certificate certificateKeyFile="${certdir}/${domain}/privkey.pem"
+                         certificateFile="${certdir}/${domain}/cert.pem"
+                         certificateChainFile="${certdir}/${domain}/fullchain.pem"
                          type="RSA" />
         </SSLHostConfig>
     </Connector>
diff --git a/meta-entrypoint.sh b/meta-entrypoint.sh
index bea0df5..afa4ebf 100644
--- a/meta-entrypoint.sh
+++ b/meta-entrypoint.sh
@@ -8,8 +8,11 @@ CREATE_SELFSIGNED=${CREATE_SELFSIGNED:-'true'}
 STAGING=${STAGING:-'false'}
 NO_COLOR=${NO_COLOR:-''}
 SELF_SIGNED_CERT_VALIDITY_DAYS=${SELF_SIGNED_CERT_VALIDITY_DAYS:-30}
-CERT_DIR=${CERT_DIR:-"/certs/"}
-export JAVA_OPTS="-Djava.awt.headless=true -XX:+UseG1GC -Dfile.encoding=UTF-8 -Ddomain=${DOMAIN}" 
+: "${CERT_DIR:="${DEHYDRATED_BASEDIR}/certs"}"
+: "${DEHYDRATED_BASEDIR:="/dehydrated"}"
+: "${DEHYDRATED_WELLKNOWN:="/static"}"
+export CERT_DIR DEHYDRATED_BASEDIR DEHYDRATED_WELLKNOWN
+export JAVA_OPTS="-Djava.awt.headless=true -XX:+UseG1GC -Dfile.encoding=UTF-8 -Dcertdir=${CERT_DIR} -Ddomain=${DOMAIN}"
 
 
 function main() {
@@ -68,6 +71,8 @@ createSelfSignedCert() {
 }
 
 function fetchCerts() {
+   mkdir -vp "$DEHYDRATED_BASEDIR"
+   mkdir -vp "$DEHYDRATED_WELLKNOWN"
 
    if [[ "${STAGING}" == "true" ]]; then
      echo 'CA="https://acme-staging-v02.api.letsencrypt.org/directory"' >> /etc/dehydrated/config
@@ -83,7 +88,7 @@ function fetchCerts() {
     
     while [[ "${SIG_INT_RECEIVED}" == 'false' ]]; do
         green "Fetching certificates"
-        dehydrated --domain ${DOMAIN} --cron --accept-terms --out ${CERT_DIR} && exitCode=$? || exitCode=$?
+        dehydrated --domain ${DOMAIN} --cron --accept-terms && exitCode=$? || exitCode=$?
         if [[ "${exitCode}" > 0 ]]; then
             red "Fetching certificates failed"
         fi
@@ -113,4 +118,4 @@ RED='\033[0;31m'
 DEFAULT_COLOR='\033[0m'
 
 
-main "$@"
\ No newline at end of file
+main "$@"