diff --git a/Dockerfile b/Dockerfile
index be0eb6c..0d6bb28 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -9,6 +9,7 @@ RUN apk add --no-cache \
         python3 py3-pip py3-setuptools py3-wheel \
         ca-certificates \
         su-exec \
+        yq \
         py3-aiohttp \
         py3-sqlalchemy \
         py3-attrs \
@@ -51,7 +52,8 @@ RUN apk add --virtual .build-deps python3-dev build-base git \
     && sed -Ei 's/psycopg2-binary.+//' optional-requirements.txt \
     && pip3 install -r requirements.txt -r optional-requirements.txt \
         dateparser langdetect python-gitlab pyquery cchardet semver tzlocal cssselect \
-    && apk del .build-deps
+    && apk del .build-deps \
+    && cp maubot/example-config.yaml . && rm -rf maubot
 # TODO also remove dateparser, langdetect and pyquery when maubot supports installing dependencies
 
 COPY . /opt/maubot
diff --git a/Dockerfile.ci b/Dockerfile.ci
index 4350c26..09bdb5f 100644
--- a/Dockerfile.ci
+++ b/Dockerfile.ci
@@ -4,6 +4,7 @@ RUN apk add --no-cache \
         python3 py3-pip py3-setuptools py3-wheel \
         ca-certificates \
         su-exec \
+        yq \
         py3-aiohttp \
         py3-sqlalchemy \
         py3-attrs \
diff --git a/docker/example-config.yaml b/docker/example-config.yaml
deleted file mode 100644
index 192a420..0000000
--- a/docker/example-config.yaml
+++ /dev/null
@@ -1,108 +0,0 @@
-# The full URI to the database. SQLite and Postgres are fully supported.
-# Other DBMSes supported by SQLAlchemy may or may not work.
-# Format examples:
-#   SQLite:   sqlite:///filename.db
-#   Postgres: postgres://username:password@hostname/dbname
-database: sqlite:////data/maubot.db
-
-# Database for encryption data.
-crypto_database:
-    # Type of database. Either "default", "pickle" or "postgres".
-    # When set to default, using SQLite as the main database will use pickle as the crypto database
-    # and using Postgres as the main database will use the same one as the crypto database.
-    #
-    # When using pickle, individual crypto databases are stored in the pickle_dir directory.
-    # When using non-default postgres, postgres_uri is used to connect to postgres.
-    type: default
-    postgres_uri: postgres://username:password@hostname/dbname
-    pickle_dir: /data/crypto
-
-plugin_directories:
-    # The directory where uploaded new plugins should be stored.
-    upload: /data/plugins
-    # The directories from which plugins should be loaded.
-    # Duplicate plugin IDs will be moved to the trash.
-    load:
-    - /data/plugins
-    # The directory where old plugin versions and conflicting plugins should be moved.
-    # Set to "delete" to delete files immediately.
-    trash: /data/trash
-    # The directory where plugin databases should be stored.
-    db: /data/plugins
-
-server:
-    # The IP and port to listen to.
-    hostname: 0.0.0.0
-    port: 29316
-    # Public base URL where the server is visible.
-    public_url: https://example.com
-    # The base management API path.
-    base_path: /_matrix/maubot/v1
-    # The base path for the UI.
-    ui_base_path: /_matrix/maubot
-    # The base path for plugin endpoints. The instance ID will be appended directly.
-    plugin_base_path: /_matrix/maubot/plugin/
-    # Override path from where to load UI resources.
-    # Set to false to using pkg_resources to find the path.
-    override_resource_path: /opt/maubot/frontend
-    # The base appservice API path. Use / for legacy appservice API and /_matrix/app/v1 for v1.
-    appservice_base_path: /_matrix/app/v1
-    # The shared secret to sign API access tokens.
-    # Set to "generate" to generate and save a new token at startup.
-    unshared_secret: generate
-
-# Shared registration secrets to allow registering new users from the management UI
-registration_secrets:
-    example.com:
-        # Client-server API URL
-        url: https://example.com
-        # registration_shared_secret from synapse config
-        secret: synapse_shared_registration_secret
-
-# List of administrator users. Plaintext passwords will be bcrypted on startup. Set empty password
-# to prevent normal login. Root is a special user that can't have a password and will always exist.
-admins:
-    root: ""
-
-# API feature switches.
-api_features:
-    login: true
-    plugin: true
-    plugin_upload: true
-    instance: true
-    instance_database: true
-    client: true
-    client_proxy: true
-    client_auth: true
-    dev_open: true
-    log: true
-
-# Python logging configuration.
-#
-# See section 16.7.2 of the Python documentation for more info:
-# https://docs.python.org/3.6/library/logging.config.html#configuration-dictionary-schema
-logging:
-    version: 1
-    formatters:
-        precise:
-            format: "[%(asctime)s] [%(levelname)s@%(name)s] %(message)s"
-    handlers:
-        file:
-            class: logging.handlers.RotatingFileHandler
-            formatter: precise
-            filename: /var/log/maubot.log
-            maxBytes: 10485760
-            backupCount: 10
-        console:
-            class: logging.StreamHandler
-            formatter: precise
-    loggers:
-        maubot:
-            level: DEBUG
-        mautrix:
-            level: DEBUG
-        aiohttp:
-            level: INFO
-    root:
-        level: DEBUG
-        handlers: [file, console]
diff --git a/docker/run.sh b/docker/run.sh
index 96a60b9..ee82283 100755
--- a/docker/run.sh
+++ b/docker/run.sh
@@ -1,21 +1,45 @@
 #!/bin/sh
 
 function fixperms {
-    chown -R $UID:$GID /var/log /data /opt/maubot
+	chown -R $UID:$GID /var/log /data /opt/maubot
+}
+
+function fixconfig {
+	# If the DB path is the default relative path, replace it with an absolute /data path
+	_db_url=$(yq e '.database' /data/config.yaml)
+	if [[ _db_url == "sqlite:///maubot.db" ]]; then
+		yq e -i '.database = "sqlite:////data/maubot.db"' /data/config.yaml
+	fi
+	_log_path=$(yq e '.logging.handlers.file.filename' /data/config.yaml)
+	if [[ _log_path == "./maubot.log" ]]; then
+		yq e -i '.logging.handlers.file.filename = "/var/log/maubot.log"' /data/config.yaml
+	fi
+	# Set the correct resource paths
+	yq e -i '
+		.server.override_resource_path = "/opt/maubot/frontend" |
+		.plugin_directories.upload = "/data/plugins" |
+		.plugin_directories.load = ["/data/plugins"] |
+		.plugin_directories.trash = "/data/trash" |
+		.plugin_directories.db = "/data/dbs"
+	' /data/config.yaml
 }
 
 cd /opt/maubot
 
-mkdir -p /var/log/maubot /data/plugins /data/trash /data/dbs /data/crypto
+mkdir -p /var/log/maubot /data/plugins /data/trash /data/dbs
 
 if [ ! -f /data/config.yaml ]; then
-	cp docker/example-config.yaml /data/config.yaml
+	cp example-config.yaml /data/config.yaml
+	# Apply some docker-specific adjustments to the config
 	echo "Config file not found. Example config copied to /data/config.yaml"
 	echo "Please modify the config file to your liking and restart the container."
 	fixperms
+	fixconfig
 	exit
 fi
 
 alembic -x config=/data/config.yaml upgrade head
 fixperms
-exec su-exec $UID:$GID python3 -m maubot -c /data/config.yaml -b docker/example-config.yaml
+fixconfig
+
+exec su-exec $UID:$GID python3 -m maubot -c /data/config.yaml