diff --git a/dev-tools/packaging/templates/linux/postinstall.sh.tmpl b/dev-tools/packaging/templates/linux/postinstall.sh.tmpl
index 9b2c5de8893..c2eb9937226 100644
--- a/dev-tools/packaging/templates/linux/postinstall.sh.tmpl
+++ b/dev-tools/packaging/templates/linux/postinstall.sh.tmpl
@@ -17,6 +17,8 @@ fi
 echo "create symlink "$symlink" to "$new_agent_dir/elastic-agent""
 ln -s "$new_agent_dir/elastic-agent" "$symlink"
 
+$new_agent_dir/elastic-agent apply-flavor
+
 # reload systemctl and then restart service
 echo "systemd enable/restart elastic-agent"
 systemctl daemon-reload 2> /dev/null
diff --git a/dev-tools/packaging/templates/linux/preinstall.sh.tmpl b/dev-tools/packaging/templates/linux/preinstall.sh.tmpl
index b396c76476c..88f13fca03b 100644
--- a/dev-tools/packaging/templates/linux/preinstall.sh.tmpl
+++ b/dev-tools/packaging/templates/linux/preinstall.sh.tmpl
@@ -5,6 +5,7 @@ set -e
 commit_hash="{{ commit_short }}"
 version_dir="{{agent_package_version}}{{snapshot_suffix}}"
 symlink="/usr/share/elastic-agent/bin/elastic-agent"
+flavor_file="/var/lib/elastic-agent/.flavor"
 new_agent_dir="/var/lib/elastic-agent/data/elastic-agent-$version_dir-$commit_hash"
 old_agent_dir=""
 
@@ -43,4 +44,19 @@ if test -L "$symlink"; then
     fi
 else
     echo "no previous installation found"
+
+    # create dir in case it does not exist
+    mkdir -p "$new_agent_dir" 
+    
+    # 2 is upgrade for Fedora, do not upgrade file when upgrading and file exists
+    if [[ "$1" != "2" ]]; then
+        if [[ -n "${ELASTIC_AGENT_FLAVOR}" ]]; then
+            # Do not modify the file if it already exists
+            echo "${ELASTIC_AGENT_FLAVOR}" > "$flavor_file"
+        else
+            # Defaults to basic installation
+            echo "basic" > "$flavor_file"
+        fi
+    fi
 fi
+
diff --git a/internal/pkg/agent/cmd/apply_flavor.go b/internal/pkg/agent/cmd/apply_flavor.go
new file mode 100644
index 00000000000..f184df21185
--- /dev/null
+++ b/internal/pkg/agent/cmd/apply_flavor.go
@@ -0,0 +1,59 @@
+// Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+// or more contributor license agreements. Licensed under the Elastic License 2.0;
+// you may not use this file except in compliance with the Elastic License 2.0.
+
+package cmd
+
+import (
+	"errors"
+	"fmt"
+	"os"
+	"path/filepath"
+
+	"github.com/spf13/cobra"
+
+	"github.com/elastic/elastic-agent/internal/pkg/agent/application/paths"
+	"github.com/elastic/elastic-agent/internal/pkg/agent/install"
+	"github.com/elastic/elastic-agent/internal/pkg/cli"
+	v1 "github.com/elastic/elastic-agent/pkg/api/v1"
+)
+
+func newApplyFlavorCommandWithArgs(_ []string, streams *cli.IOStreams) *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "apply-flavor",
+		Short: "Apply Flavor cleans up unnecessary components from agent installation directory",
+		Run: func(c *cobra.Command, _ []string) {
+			if err := applyCmd(); err != nil {
+				fmt.Fprintf(streams.Err, "Error: %v\n%s\n", err, troubleshootMessage())
+				logExternal(fmt.Sprintf("%s apply flavor failed: %s", paths.BinaryName, err))
+				os.Exit(1)
+			}
+		},
+		Hidden: true,
+	}
+
+	return cmd
+}
+
+func applyCmd() error {
+	topPath := paths.Top()
+	detectedFlavor, err := install.UsedFlavor(topPath, "")
+	if err != nil {
+		if errors.Is(err, os.ErrNotExist) {
+			return nil
+		}
+		return err
+	}
+	if detectedFlavor == "" {
+		return nil
+	}
+
+	versionedHome := paths.VersionedHome(topPath)
+	manifestFilePath := filepath.Join(versionedHome, v1.ManifestFileName)
+	flavor, err := install.Flavor(detectedFlavor, manifestFilePath, nil)
+	if err != nil {
+		return err
+	}
+
+	return install.ApplyFlavor(versionedHome, flavor)
+}
diff --git a/internal/pkg/agent/cmd/common.go b/internal/pkg/agent/cmd/common.go
index 059c144399d..0bec7dc3540 100644
--- a/internal/pkg/agent/cmd/common.go
+++ b/internal/pkg/agent/cmd/common.go
@@ -94,6 +94,7 @@ func NewCommandWithArgs(args []string, streams *cli.IOStreams) *cobra.Command {
 	addCommandIfNotNil(cmd, newComponentCommandWithArgs(args, streams))
 	addCommandIfNotNil(cmd, newLogsCommandWithArgs(args, streams))
 	addCommandIfNotNil(cmd, newOtelCommandWithArgs(args, streams))
+	addCommandIfNotNil(cmd, newApplyFlavorCommandWithArgs(args, streams))
 
 	// windows special hidden sub-command (only added on Windows)
 	reexec := newReExecWindowsCommand(args, streams)
diff --git a/internal/pkg/agent/install/.flavors b/internal/pkg/agent/install/.flavors
new file mode 100644
index 00000000000..42358f5c5a4
--- /dev/null
+++ b/internal/pkg/agent/install/.flavors
@@ -0,0 +1,13 @@
+basic:
+  - agentbeat
+  - endpoint-security
+  - pf-host-agent
+servers:
+  - agentbeat
+  - endpoint-security
+  - pf-host-agent
+  - cloudbeat
+  - apm-server
+  - fleet-server
+  - pf-elastic-symbolizer
+  - pf-elastic-collector
diff --git a/internal/pkg/agent/install/flavors.go b/internal/pkg/agent/install/flavors.go
index 61f84124ce9..b90e2203387 100644
--- a/internal/pkg/agent/install/flavors.go
+++ b/internal/pkg/agent/install/flavors.go
@@ -48,7 +48,7 @@ func UsedFlavor(topPath, defaultFlavor string) (string, error) {
 		return "", err
 	}
 
-	return string(content), nil
+	return strings.TrimSpace(string(content)), nil
 }
 
 func Flavor(detectedFlavor string, registryPath string, flavorsRegistry map[string][]string) (FlavorDefinition, error) {