diff --git a/charts/deckhand/values.yaml b/charts/deckhand/values.yaml
index d4a8e44c..48319e3e 100644
--- a/charts/deckhand/values.yaml
+++ b/charts/deckhand/values.yaml
@@ -216,7 +216,6 @@ conf:
   deckhand:
     DEFAULT:
       debug: true
-      log_file: deckhand.log
       use_stderr: true
       use_syslog: true
     database:
@@ -232,27 +231,34 @@ conf:
       policy_dirs: policy.d
   logging:
     loggers:
-      keys: 'root, deckhand'
+      keys: 'root, deckhand, error'
     handlers:
-      keys: 'file, null, syslog'
+      keys: 'null, stderr, stdout, syslog'
     formatters:
       keys: 'simple, context'
     logger_deckhand:
       level: DEBUG
-      handlers: file
+      handlers: stdout
+      qualname: deckhand
+    logger_error:
+      level: ERROR
+      handlers: stderr
       qualname: deckhand
     logger_root:
       level: WARNING
       handlers: null
-    handler_file:
-      class: FileHandler
-      level: DEBUG
-      args: "('deckhand.log', 'w+')"
-      formatter: context
     handler_null:
       class: 'logging.NullHandler'
       formatter: context
       args: '()'
+    handler_stderr:
+      class: StreamHandler
+      args: '(sys.stderr,)'
+      formatter: context
+    handler_stdout:
+      class: StreamHandler
+      args: '(sys.stdout,)'
+      formatter: context
     handler_syslog:
       class: 'handlers.SysLogHandler'
       level: ERROR
diff --git a/tools/functional-tests.sh b/tools/functional-tests.sh
index 5833b7e5..d63e392e 100755
--- a/tools/functional-tests.sh
+++ b/tools/functional-tests.sh
@@ -75,7 +75,7 @@ function gen_config {
 # Create a logging config file to dump everything to stdout/stderr.
 cat <<EOCONF > $CONF_DIR/logging.conf
 [loggers]
-keys = root, deckhand
+keys = root, deckhand, error
 
 [handlers]
 keys = null, stderr, stdout
@@ -88,6 +88,10 @@ level = DEBUG
 handlers = stdout
 qualname = deckhand
 
+[logger_error]
+level = ERROR
+handlers = stderr
+
 [logger_root]
 level = WARNING
 handlers = null
@@ -118,9 +122,6 @@ EOCONF
 cat <<EOCONF > $CONF_DIR/deckhand.conf
 [DEFAULT]
 debug = true
-# NOTE: Use the location of this file inside the mounted volume in the
-# container.
-log_config_append = /etc/deckhand/logging.conf
 publish_errors = true
 use_stderr = true
 # NOTE: allow_anonymous_access allows these functional tests to get around
@@ -148,6 +149,12 @@ connection = $DATABASE_URL
 # auth_type = password
 EOCONF
 
+# Only set up logging if running Deckhand via uwsgi. The container already has
+# values for logging.
+if [ -z "$DECKHAND_IMAGE" ]; then
+    sed '1 a log_config_append = '"$CONF_DIR"'/logging.conf' $CONF_DIR/deckhand.conf
+fi
+
     echo $CONF_DIR/deckhand.conf 1>&2
     cat $CONF_DIR/deckhand.conf 1>&2
 
@@ -185,10 +192,8 @@ gen_config
 gen_paste
 gen_policy
 
-log_section Starting Deckhand image
-
 if [ -z "$DECKHAND_IMAGE" ]; then
-    echo "Running Deckhand via uwsgi"
+    log_section "Running Deckhand via uwsgi"
 
     # Set --workers 2, so that concurrency is always tested.
     uwsgi \
@@ -201,7 +206,7 @@ if [ -z "$DECKHAND_IMAGE" ]; then
     -L \
     --pyargv "--config-file $CONF_DIR/deckhand.conf" &> $STDOUT &
 else
-    echo "Running Deckhand via Docker"
+    log_section "Running Deckhand via Docker"
     sudo docker run \
         --rm \
         --net=host \