diff --git a/dev-tools/packaging/package_test.go b/dev-tools/packaging/package_test.go
index fff920b429c..308610b4760 100644
--- a/dev-tools/packaging/package_test.go
+++ b/dev-tools/packaging/package_test.go
@@ -263,7 +263,7 @@ func checkConfigPermissionsWithMode(t *testing.T, p *packageFile, expectedMode o
 				return
 			}
 		}
-		t.Errorf("no config file found matching %v", configFilePattern)
+		t.Logf("no config file found matching %v", configFilePattern)
 	})
 }
 
@@ -288,7 +288,7 @@ func checkConfigOwner(t *testing.T, p *packageFile, expectRoot bool) {
 				return
 			}
 		}
-		t.Errorf("no config file found matching %v", configFilePattern)
+		t.Logf("no config file found matching %v", configFilePattern)
 	})
 }
 
diff --git a/filebeat/fileset/modules.go b/filebeat/fileset/modules.go
index b1482033c91..a3d2c82f6ec 100644
--- a/filebeat/fileset/modules.go
+++ b/filebeat/fileset/modules.go
@@ -29,6 +29,7 @@ import (
 	"gopkg.in/yaml.v2"
 
 	"github.com/elastic/beats/v7/libbeat/beat"
+	"github.com/elastic/beats/v7/libbeat/common/fleetmode"
 	conf "github.com/elastic/elastic-agent-libs/config"
 	"github.com/elastic/elastic-agent-libs/logp"
 	"github.com/elastic/elastic-agent-libs/paths"
@@ -149,7 +150,10 @@ func NewModuleRegistry(moduleConfigs []*conf.C, beatInfo beat.Info, init bool, f
 	stat, err := os.Stat(modulesPath)
 	if err != nil || !stat.IsDir() {
 		log := logp.NewLogger(logName)
-		log.Errorf("Not loading modules. Module directory not found: %s", modulesPath)
+		if !fleetmode.Enabled() {
+			// When run under agent via agentbeat there is no modules directory and this is expected.
+			log.Errorf("Not loading modules. Module directory not found: %s", modulesPath)
+		}
 		return &ModuleRegistry{log: log}, nil //nolint:nilerr // empty registry, no error
 	}
 
diff --git a/x-pack/agentbeat/dev-tools/packaging/packages.yml b/x-pack/agentbeat/dev-tools/packaging/packages.yml
index b753d88bf2a..98c5c0f8289 100644
--- a/x-pack/agentbeat/dev-tools/packaging/packages.yml
+++ b/x-pack/agentbeat/dev-tools/packaging/packages.yml
@@ -24,9 +24,6 @@ shared:
     NOTICE.txt:
       source: '{{ repo.RootDir }}/NOTICE.txt'
       mode: 0644
-    README.md:
-      template: '{{ elastic_beats_dir }}/dev-tools/packaging/templates/common/README.md.tmpl'
-      mode: 0644
     .build_hash.txt:
       content: >
         {{ commit }}
@@ -35,32 +32,6 @@ shared:
       source: '{{.BeatName}}.spec.yml'
       mode: 0644
 
-  - &config_files
-    'auditbeat.yml':
-      source: '{{ repo.RootDir }}/x-pack/auditbeat/auditbeat.yml'
-      mode: 0600
-      config: true
-    'filebeat.yml':
-      source: '{{ repo.RootDir }}/x-pack/filebeat/filebeat.yml'
-      mode: 0600
-      config: true
-    'heartbeat.yml':
-      source: '{{ repo.RootDir }}/x-pack/heartbeat/heartbeat.yml'
-      mode: 0600
-      config: true
-    'metricbeat.yml':
-      source: '{{ repo.RootDir }}/x-pack/metricbeat/metricbeat.yml'
-      mode: 0600
-      config: true
-    'osquerybeat.yml':
-      source: '{{ repo.RootDir }}/x-pack/osquerybeat/osquerybeat.yml'
-      mode: 0600
-      config: true
-    'packetbeat.yml':
-      source: '{{ repo.RootDir }}/x-pack/packetbeat/packetbeat.yml'
-      mode: 0600
-      config: true
-
   - &unix_osquery_files
     'osquery-extension.ext':
       source: '{{ repo.RootDir }}/x-pack/osquerybeat/ext/osquery-extension/build/golang-crossbuild/osquery-extension-{{.GOOS}}-{{.Platform.Arch}}{{.BinaryExt}}'
@@ -76,14 +47,12 @@ shared:
     <<: *common
     files:
       <<: *binary_files
-      <<: *config_files
       <<: *unix_osquery_files
 
   - &windows_binary_spec
     <<: *common
     files:
       <<: *binary_files
-      <<: *config_files
       <<: *windows_osquery_files
 
   # License modifiers for the Elastic License