diff --git a/CHANGELOG.md b/CHANGELOG.md
index 17da56b757..5b9c12fb08 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 ### Fixed
 
-- Make sure the daemonset can start in GKE Autopiot (#602)
+- Make sure the daemonset can start in GKE Autopiot (#608)
+- Make containerd engine default in for fluentd logs and use always use it in GKE Autopiot (#609)
 
 ## [0.66.1] - 2022-12-08
 
diff --git a/helm-charts/splunk-otel-collector/templates/configmap-fluentd-cri.yaml b/helm-charts/splunk-otel-collector/templates/configmap-fluentd-cri.yaml
deleted file mode 100644
index 85ef3bb6f1..0000000000
--- a/helm-charts/splunk-otel-collector/templates/configmap-fluentd-cri.yaml
+++ /dev/null
@@ -1,51 +0,0 @@
-{{ $agent := fromYaml (include "splunk-otel-collector.agent" .) }}
-{{- if and (eq (include "splunk-otel-collector.logsEnabled" .) "true") $agent.enabled (eq .Values.logsEngine "fluentd") }}
-{{/*
-Fluentd config parts applied only to clusters with containerd/cri-o runtime.
-*/}}
-apiVersion: v1
-kind: ConfigMap
-metadata:
-  name: {{ template "splunk-otel-collector.fullname" . }}-fluentd-cri
-  labels:
-    {{- include "splunk-otel-collector.commonLabels" . | nindent 4 }}
-    app: {{ template "splunk-otel-collector.name" . }}
-    chart: {{ template "splunk-otel-collector.chart" . }}
-    release: {{ .Release.Name }}
-    heritage: {{ .Release.Service }}
-data:
-
-  source.containers.parse.conf: |-
-    @type regexp
-    expression /^(?<time>.+) (?<stream>stdout|stderr)( (?<partial_flag>[FP]))? (?<log>.*)$/
-    time_format {{ .Values.fluentd.config.containers.criTimeFormat }}
-
-  output.filter.conf: |-
-    # = handle cri/containerd multiline format =
-    <filter tail.containers.var.log.containers.**>
-      @type concat
-      key log
-      partial_key partial_flag
-      partial_value P
-      separator ''
-      timeout_label @SPLUNK
-    </filter>
-
-  output.transform.conf: |-
-    # extract pod_uid and container_name for CRIO runtime
-    # currently CRI does not produce log paths with all the necessary
-    # metadata to parse out pod, namespace, container_name, container_id.
-    # this may be resolved in the future by this issue: https://github.com/kubernetes/kubernetes/issues/58638#issuecomment-385126031
-    <filter tail.containers.var.log.pods.**>
-      @type jq_transformer
-      jq '.record | . + (.source | capture("/var/log/pods/(?<pod_uid>[^/]+)/(?<container_name>[^/]+)/(?<container_retry>[0-9]+).log")) | .sourcetype = ("kube:container:" + .container_name)'
-    </filter>
-    # rename pod_uid and container_name to otel semantics.
-    <filter tail.containers.var.log.pods.**>
-      @type record_transformer
-      <record>
-        k8s.pod.uid ${record["pod_uid"]}
-        k8s.container.name ${record["container_name"]}
-      </record>
-    </filter>
-{{- end }}
diff --git a/helm-charts/splunk-otel-collector/templates/configmap-fluentd.yaml b/helm-charts/splunk-otel-collector/templates/configmap-fluentd.yaml
index c8535b0ccf..c6cf77cf57 100644
--- a/helm-charts/splunk-otel-collector/templates/configmap-fluentd.yaml
+++ b/helm-charts/splunk-otel-collector/templates/configmap-fluentd.yaml
@@ -282,4 +282,40 @@ data:
         </format>
       </match>
     </label>
+
+  {{- /*
+    Default configuration files for CRI container engine.
+    Can be overridden for docker engine by prepare-fluentd-config container.
+  */}}
+  source.containers.parse.conf: |-
+    @type regexp
+    expression /^(?<time>.+) (?<stream>stdout|stderr)( (?<partial_flag>[FP]))? (?<log>.*)$/
+    time_format {{ .Values.fluentd.config.containers.criTimeFormat }}
+  output.filter.conf: |-
+    # = handle cri/containerd multiline format =
+    <filter tail.containers.var.log.containers.**>
+      @type concat
+      key log
+      partial_key partial_flag
+      partial_value P
+      separator ''
+      timeout_label @SPLUNK
+    </filter>
+  output.transform.conf: |-
+    # extract pod_uid and container_name for CRIO runtime
+    # currently CRI does not produce log paths with all the necessary
+    # metadata to parse out pod, namespace, container_name, container_id.
+    # this may be resolved in the future by this issue: https://github.com/kubernetes/kubernetes/issues/58638#issuecomment-385126031
+    <filter tail.containers.var.log.pods.**>
+      @type jq_transformer
+      jq '.record | . + (.source | capture("/var/log/pods/(?<pod_uid>[^/]+)/(?<container_name>[^/]+)/(?<container_retry>[0-9]+).log")) | .sourcetype = ("kube:container:" + .container_name)'
+    </filter>
+    # rename pod_uid and container_name to otel semantics.
+    <filter tail.containers.var.log.pods.**>
+      @type record_transformer
+      <record>
+        k8s.pod.uid ${record["pod_uid"]}
+        k8s.container.name ${record["container_name"]}
+      </record>
+    </filter>
 {{- end }}
diff --git a/helm-charts/splunk-otel-collector/templates/daemonset.yaml b/helm-charts/splunk-otel-collector/templates/daemonset.yaml
index 90c8dcff61..4bfbbbc12a 100644
--- a/helm-charts/splunk-otel-collector/templates/daemonset.yaml
+++ b/helm-charts/splunk-otel-collector/templates/daemonset.yaml
@@ -70,7 +70,7 @@ spec:
       {{- end }}
       {{- if and (eq (include "splunk-otel-collector.logsEnabled" .) "true") (not .Values.isWindows) }}
       initContainers:
-        {{- if (eq .Values.logsEngine "fluentd") }}
+        {{- if and (eq .Values.logsEngine "fluentd") (not (eq .Values.distribution "gke/autopilot")) }}
         - name: prepare-fluentd-config
           image: {{ template "splunk-otel-collector.image.fluentd" . }}
           imagePullPolicy: {{ .Values.image.fluentd.pullPolicy }}
@@ -78,14 +78,11 @@ spec:
           securityContext:
             runAsUser: 0
           args:
-            - if [ -z "${LOG_FORMAT_TYPE}" ]; then
-                if [ "$(ls {{ .Values.fluentd.config.containers.pathDest }}/*/*json.log 2>/dev/null | wc -l)" != "0" ]; then
-                  export LOG_FORMAT_TYPE=json;
-                else
-                  export LOG_FORMAT_TYPE=cri;
-                fi;
+            - cp /fluentd/etc/common/* /fluentd/etc/;
+              {{- /* Update fluentd configs if docker engine is configured or discovered from existing log files. */}}
+              if [ "${LOG_FORMAT_TYPE}" == "json" ] || [ "$(ls {{ .Values.fluentd.config.containers.pathDest }}/*/*json.log 2>/dev/null | wc -l)" != "0" ]; then
+                  cp /fluentd/etc/json/* /fluentd/etc/;
               fi;
-              cp /fluentd/etc/common/* /fluentd/etc/${LOG_FORMAT_TYPE}/* /fluentd/etc/
           env:
             - name: LOG_FORMAT_TYPE
               value: "{{ .Values.fluentd.config.containers.logFormatType }}"
@@ -99,8 +96,6 @@ spec:
               mountPath: /fluentd/etc/common
             - name: fluentd-config-json
               mountPath: /fluentd/etc/json
-            - name: fluentd-config-cri
-              mountPath: /fluentd/etc/cri
         {{- else }}
         {{- if not (eq .Values.distribution "gke/autopilot") }}
         - name: migrate-checkpoint
@@ -412,8 +407,10 @@ spec:
         hostPath:
           path: {{ .Values.fluentd.config.journalLogPath | quote }}
       - name: fluentd-config
+      {{- if (not (eq .Values.distribution "gke/autopilot")) }}
         emptyDir: {}
       - name: fluentd-config-common
+      {{- end }}
         configMap:
           name: {{ template "splunk-otel-collector.fullname" . }}-fluentd
       - name: fluentd-config-cri
diff --git a/rendered/manifests/logs-only/configmap-fluentd-cri.yaml b/rendered/manifests/logs-only/configmap-fluentd-cri.yaml
deleted file mode 100644
index 6374b39628..0000000000
--- a/rendered/manifests/logs-only/configmap-fluentd-cri.yaml
+++ /dev/null
@@ -1,51 +0,0 @@
----
-# Source: splunk-otel-collector/templates/configmap-fluentd-cri.yaml
-apiVersion: v1
-kind: ConfigMap
-metadata:
-  name: default-splunk-otel-collector-fluentd-cri
-  labels:
-    app.kubernetes.io/name: splunk-otel-collector
-    helm.sh/chart: splunk-otel-collector-0.66.1
-    app.kubernetes.io/managed-by: Helm
-    app.kubernetes.io/instance: default
-    app.kubernetes.io/version: "0.66.0"
-    app: splunk-otel-collector
-    chart: splunk-otel-collector-0.66.1
-    release: default
-    heritage: Helm
-data:
-
-  source.containers.parse.conf: |-
-    @type regexp
-    expression /^(?<time>.+) (?<stream>stdout|stderr)( (?<partial_flag>[FP]))? (?<log>.*)$/
-    time_format %Y-%m-%dT%H:%M:%S.%N%:z
-
-  output.filter.conf: |-
-    # = handle cri/containerd multiline format =
-    <filter tail.containers.var.log.containers.**>
-      @type concat
-      key log
-      partial_key partial_flag
-      partial_value P
-      separator ''
-      timeout_label @SPLUNK
-    </filter>
-
-  output.transform.conf: |-
-    # extract pod_uid and container_name for CRIO runtime
-    # currently CRI does not produce log paths with all the necessary
-    # metadata to parse out pod, namespace, container_name, container_id.
-    # this may be resolved in the future by this issue: https://github.com/kubernetes/kubernetes/issues/58638#issuecomment-385126031
-    <filter tail.containers.var.log.pods.**>
-      @type jq_transformer
-      jq '.record | . + (.source | capture("/var/log/pods/(?<pod_uid>[^/]+)/(?<container_name>[^/]+)/(?<container_retry>[0-9]+).log")) | .sourcetype = ("kube:container:" + .container_name)'
-    </filter>
-    # rename pod_uid and container_name to otel semantics.
-    <filter tail.containers.var.log.pods.**>
-      @type record_transformer
-      <record>
-        k8s.pod.uid ${record["pod_uid"]}
-        k8s.container.name ${record["container_name"]}
-      </record>
-    </filter>
diff --git a/rendered/manifests/logs-only/configmap-fluentd.yaml b/rendered/manifests/logs-only/configmap-fluentd.yaml
index ed730c3cdb..532a6f522c 100644
--- a/rendered/manifests/logs-only/configmap-fluentd.yaml
+++ b/rendered/manifests/logs-only/configmap-fluentd.yaml
@@ -319,3 +319,34 @@ data:
         </format>
       </match>
     </label>
+  source.containers.parse.conf: |-
+    @type regexp
+    expression /^(?<time>.+) (?<stream>stdout|stderr)( (?<partial_flag>[FP]))? (?<log>.*)$/
+    time_format %Y-%m-%dT%H:%M:%S.%N%:z
+  output.filter.conf: |-
+    # = handle cri/containerd multiline format =
+    <filter tail.containers.var.log.containers.**>
+      @type concat
+      key log
+      partial_key partial_flag
+      partial_value P
+      separator ''
+      timeout_label @SPLUNK
+    </filter>
+  output.transform.conf: |-
+    # extract pod_uid and container_name for CRIO runtime
+    # currently CRI does not produce log paths with all the necessary
+    # metadata to parse out pod, namespace, container_name, container_id.
+    # this may be resolved in the future by this issue: https://github.com/kubernetes/kubernetes/issues/58638#issuecomment-385126031
+    <filter tail.containers.var.log.pods.**>
+      @type jq_transformer
+      jq '.record | . + (.source | capture("/var/log/pods/(?<pod_uid>[^/]+)/(?<container_name>[^/]+)/(?<container_retry>[0-9]+).log")) | .sourcetype = ("kube:container:" + .container_name)'
+    </filter>
+    # rename pod_uid and container_name to otel semantics.
+    <filter tail.containers.var.log.pods.**>
+      @type record_transformer
+      <record>
+        k8s.pod.uid ${record["pod_uid"]}
+        k8s.container.name ${record["container_name"]}
+      </record>
+    </filter>
diff --git a/rendered/manifests/logs-only/daemonset.yaml b/rendered/manifests/logs-only/daemonset.yaml
index 8b21c2773f..27f9274eef 100644
--- a/rendered/manifests/logs-only/daemonset.yaml
+++ b/rendered/manifests/logs-only/daemonset.yaml
@@ -30,7 +30,7 @@ spec:
         app: splunk-otel-collector
         release: default
       annotations:
-        checksum/config: 0640e5c5b99d34b55fbd125d1c34fab8387b37d8c3c5a1e7c6857867a6ad7dfc
+        checksum/config: 0dd2001a5452e85b22ed2a419f03895f9b0a0382fb9d035be838299393f6080b
         kubectl.kubernetes.io/default-container: otel-collector
     spec:
       hostNetwork: true
@@ -50,14 +50,10 @@ spec:
           securityContext:
             runAsUser: 0
           args:
-            - if [ -z "${LOG_FORMAT_TYPE}" ]; then
-                if [ "$(ls /var/lib/docker/containers/*/*json.log 2>/dev/null | wc -l)" != "0" ]; then
-                  export LOG_FORMAT_TYPE=json;
-                else
-                  export LOG_FORMAT_TYPE=cri;
-                fi;
+            - cp /fluentd/etc/common/* /fluentd/etc/;
+              if [ "${LOG_FORMAT_TYPE}" == "json" ] || [ "$(ls /var/lib/docker/containers/*/*json.log 2>/dev/null | wc -l)" != "0" ]; then
+                  cp /fluentd/etc/json/* /fluentd/etc/;
               fi;
-              cp /fluentd/etc/common/* /fluentd/etc/${LOG_FORMAT_TYPE}/* /fluentd/etc/
           env:
             - name: LOG_FORMAT_TYPE
               value: ""
@@ -71,8 +67,6 @@ spec:
               mountPath: /fluentd/etc/common
             - name: fluentd-config-json
               mountPath: /fluentd/etc/json
-            - name: fluentd-config-cri
-              mountPath: /fluentd/etc/cri
       containers:
       - name: fluentd
         image: splunk/fluentd-hec:1.2.8