diff --git a/compose/compose.env b/compose/compose.env
index db896b33c..d514f8ea5 100644
--- a/compose/compose.env
+++ b/compose/compose.env
@@ -15,11 +15,11 @@ COMPOSE_KOMODO_IMAGE_TAG=latest
 COMPOSE_LOGGING_DRIVER=local # Enable log rotation with the local driver.
 
 ## DB credentials - Ignored for Sqlite
-DB_USERNAME=admin
-DB_PASSWORD=admin
+KOMODO_DB_USERNAME=admin
+KOMODO_DB_PASSWORD=admin
 
 ## Configure a secure passkey to authenticate between Core / Periphery.
-PASSKEY=a_random_passkey
+KOMODO_PASSKEY=a_random_passkey
 
 #=-------------------------=#
 #= Komodo Core Environment =#
@@ -52,8 +52,6 @@ KOMODO_MONITORING_INTERVAL="15-sec"
 ## Default: 5-min
 KOMODO_RESOURCE_POLL_INTERVAL="5-min"
 
-## Used to auth against periphery. Alt: KOMODO_PASSKEY_FILE
-KOMODO_PASSKEY=${PASSKEY}
 ## Used to auth incoming webhooks. Alt: KOMODO_WEBHOOK_SECRET_FILE
 KOMODO_WEBHOOK_SECRET=a_random_secret
 ## Used to generate jwt. Alt: KOMODO_JWT_SECRET_FILE
@@ -115,8 +113,11 @@ KOMODO_HETZNER_TOKEN= # Alt: KOMODO_HETZNER_TOKEN_FILE
 ## Full variable list + descriptions are available here:
 ## 🦎 https://github.com/mbecker20/komodo/blob/main/config/periphery.config.toml 🦎
 
-## Periphery passkeys must include KOMODO_PASSKEY to authenticate
-PERIPHERY_PASSKEYS=${PASSKEY}
+## Periphery passkeys must include KOMODO_PASSKEY to authenticate.
+PERIPHERY_PASSKEYS=${KOMODO_PASSKEY}
+
+## Specify the root directory used by Periphery agent.
+PERIPHERY_ROOT_DIRECTORY=/etc/komodo
 
 ## Enable SSL using self signed certificates.
 ## Connect to Periphery at https://address:8120.
diff --git a/compose/mongo.compose.yaml b/compose/mongo.compose.yaml
index 2ce734f6f..4045b7962 100644
--- a/compose/mongo.compose.yaml
+++ b/compose/mongo.compose.yaml
@@ -43,8 +43,8 @@ services:
     env_file: ./compose.env
     environment:
       KOMODO_DATABASE_ADDRESS: mongo:27017
-      KOMODO_DATABASE_USERNAME: ${DB_USERNAME}
-      KOMODO_DATABASE_PASSWORD: ${DB_PASSWORD}
+      KOMODO_DATABASE_USERNAME: ${KOMODO_DB_USERNAME}
+      KOMODO_DATABASE_PASSWORD: ${KOMODO_DB_PASSWORD}
     volumes:
       ## Core cache for repos for latest commit hash / contents
       - repo-cache:/repo-cache
@@ -70,22 +70,21 @@ services:
     networks:
       - default
     env_file: ./compose.env
+    environment:
+      PERIPHERY_REPO_DIR: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/repos
+      PERIPHERY_STACK_DIR: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/stacks
+      PERIPHERY_SSL_KEY_FILE: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/ssl/key.pem
+      PERIPHERY_SSL_CERT_FILE: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/ssl/cert.pem
     volumes:
       ## Mount external docker socket
       - /var/run/docker.sock:/var/run/docker.sock
       ## Allow Periphery to see processes outside of container
       - /proc:/proc
-      ## use self signed certs in docker volume, 
-      ## or mount your own signed certs.
-      - ssl-certs:/etc/komodo/ssl
-      ## manage repos in a docker volume, 
-      ## or change it to an accessible host directory.
-      - repos:/etc/komodo/repos
-      ## manage stack files in a docker volume, 
-      ## or change it to an accessible host directory.
-      - stacks:/etc/komodo/stacks
-      ## Optionally mount a path to store compose files
-      # - /path/to/compose:/host/compose
+      ## Specify the Periphery agent root directory.
+      ## Must be the same inside and outside the container,
+      ## or docker will get confused. See https://github.com/mbecker20/komodo/discussions/180.
+      ## Default: /etc/komodo.
+      - ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}:${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}
 
 volumes:
   # Mongo
@@ -93,10 +92,6 @@ volumes:
   mongo-config:
   # Core
   repo-cache:
-  # Periphery
-  ssl-certs:
-  repos:
-  stacks:
 
 networks:
   default: {}
\ No newline at end of file
diff --git a/compose/postgres.compose.yaml b/compose/postgres.compose.yaml
index bce6e49a7..aec0dc05c 100644
--- a/compose/postgres.compose.yaml
+++ b/compose/postgres.compose.yaml
@@ -3,7 +3,7 @@
 ###################################
 
 ## This compose file will deploy:
-##   1. Postgres + FerretDB Mongo adapter
+##   1. Postgres + FerretDB Mongo adapter (https://www.ferretdb.com)
 ##   2. Komodo Core
 ##   3. Komodo Periphery
 
@@ -57,7 +57,7 @@ services:
       - 9120:9120
     env_file: ./compose.env
     environment:
-      KOMODO_DATABASE_URI: mongodb://${DB_USERNAME}:${DB_PASSWORD}@ferretdb:27017/${KOMODO_DATABASE_DB_NAME:-komodo}?authMechanism=PLAIN
+      KOMODO_DATABASE_URI: mongodb://${KOMODO_DB_USERNAME}:${KOMODO_DB_PASSWORD}@ferretdb:27017/${KOMODO_DATABASE_DB_NAME:-komodo}?authMechanism=PLAIN
     volumes:
       ## Core cache for repos for latest commit hash / contents
       - repo-cache:/repo-cache
@@ -83,32 +83,27 @@ services:
     networks:
       - default
     env_file: ./compose.env
+    environment:
+      PERIPHERY_REPO_DIR: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/repos
+      PERIPHERY_STACK_DIR: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/stacks
+      PERIPHERY_SSL_KEY_FILE: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/ssl/key.pem
+      PERIPHERY_SSL_CERT_FILE: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/ssl/cert.pem
     volumes:
       ## Mount external docker socket
       - /var/run/docker.sock:/var/run/docker.sock
       ## Allow Periphery to see processes outside of container
       - /proc:/proc
-      ## use self signed certs in docker volume, 
-      ## or mount your own signed certs.
-      - ssl-certs:/etc/komodo/ssl
-      ## manage repos in a docker volume, 
-      ## or change it to an accessible host directory.
-      - repos:/etc/komodo/repos
-      ## manage stack files in a docker volume, 
-      ## or change it to an accessible host directory.
-      - stacks:/etc/komodo/stacks
-      ## Optionally mount a path to store compose files
-      # - /path/to/compose:/host/compose
+      ## Specify the Periphery agent root directory.
+      ## Must be the same inside and outside the container,
+      ## or docker will get confused. See https://github.com/mbecker20/komodo/discussions/180.
+      ## Default: /etc/komodo.
+      - ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}:${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}
 
 volumes:
   # Postgres
   pg-data:
   # Core
   repo-cache:
-  # Periphery
-  ssl-certs:
-  repos:
-  stacks:
 
 networks:
   default: {}
\ No newline at end of file
diff --git a/compose/sqlite.compose.yaml b/compose/sqlite.compose.yaml
index 6a41260e0..54739f425 100644
--- a/compose/sqlite.compose.yaml
+++ b/compose/sqlite.compose.yaml
@@ -3,7 +3,7 @@
 #################################
 
 ## This compose file will deploy:
-##   1. Sqlite + FerretDB Mongo adapter
+##   1. Sqlite + FerretDB Mongo adapter (https://www.ferretdb.com)
 ##   2. Komodo Core
 ##   3. Komodo Periphery
 
@@ -65,32 +65,27 @@ services:
     networks:
       - default
     env_file: ./compose.env
+    environment:
+      PERIPHERY_REPO_DIR: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/repos
+      PERIPHERY_STACK_DIR: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/stacks
+      PERIPHERY_SSL_KEY_FILE: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/ssl/key.pem
+      PERIPHERY_SSL_CERT_FILE: ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}/ssl/cert.pem
     volumes:
       ## Mount external docker socket
       - /var/run/docker.sock:/var/run/docker.sock
       ## Allow Periphery to see processes outside of container
       - /proc:/proc
-      ## use self signed certs in docker volume, 
-      ## or mount your own signed certs.
-      - ssl-certs:/etc/komodo/ssl
-      ## manage repos in a docker volume, 
-      ## or change it to an accessible host directory.
-      - repos:/etc/komodo/repos
-      ## manage stack files in a docker volume, 
-      ## or change it to an accessible host directory.
-      - stacks:/etc/komodo/stacks
-      ## Optionally mount a path to store compose files
-      # - /path/to/compose:/host/compose
+      ## Specify the Periphery agent root directory.
+      ## Must be the same inside and outside the container,
+      ## or docker will get confused. See https://github.com/mbecker20/komodo/discussions/180.
+      ## Default: /etc/komodo.
+      - ${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}:${PERIPHERY_ROOT_DIRECTORY:-/etc/komodo}
 
 volumes:
   # Sqlite
   sqlite-data:
   # Core
   repo-cache:
-  # Periphery
-  ssl-certs:
-  repos:
-  stacks:
 
 networks:
   default: {}
\ No newline at end of file