diff --git a/cmd/security-agent/subcommands/runtime/command.go b/cmd/security-agent/subcommands/runtime/command.go
index ae5b752996f7c..afeaf89a312d7 100644
--- a/cmd/security-agent/subcommands/runtime/command.go
+++ b/cmd/security-agent/subcommands/runtime/command.go
@@ -9,6 +9,8 @@
 package runtime
 
 import (
+	"archive/zip"
+	"bytes"
 	"context"
 	"encoding/json"
 	"errors"
@@ -17,6 +19,7 @@ import (
 	"os"
 	"path"
 	"runtime"
+	"strings"
 	"time"
 
 	"github.com/spf13/cobra"
@@ -186,6 +189,7 @@ type downloadPolicyCliParams struct {
 
 	check      bool
 	outputPath string
+	source     string
 }
 
 func downloadPolicyCommands(globalParams *command.GlobalParams) []*cobra.Command {
@@ -210,6 +214,7 @@ func downloadPolicyCommands(globalParams *command.GlobalParams) []*cobra.Command
 
 	downloadPolicyCmd.Flags().BoolVar(&downloadPolicyArgs.check, "check", false, "Check policies after downloading")
 	downloadPolicyCmd.Flags().StringVar(&downloadPolicyArgs.outputPath, "output-path", "", "Output path for downloaded policies")
+	downloadPolicyCmd.Flags().StringVar(&downloadPolicyArgs.source, "source", "all", `Specify wether should download the custom, default or all policies. allowed: "all", "default", "custom"`)
 
 	return []*cobra.Command{downloadPolicyCmd}
 }
@@ -765,7 +770,36 @@ func downloadPolicy(log log.Component, config config.Component, _ secrets.Compon
 	if err != nil {
 		return err
 	}
+
+	// Unzip the downloaded file containing both default and custom policies
 	resBytes := []byte(res)
+	reader, err := zip.NewReader(bytes.NewReader(resBytes), int64(len(resBytes)))
+	if err != nil {
+		return err
+	}
+
+	var defaultPolicy []byte
+	var customPolicies []string
+
+	for _, file := range reader.File {
+		if strings.HasSuffix(file.Name, ".policy") {
+			pf, err := file.Open()
+			if err != nil {
+				return err
+			}
+			policyData, err := io.ReadAll(pf)
+			pf.Close()
+			if err != nil {
+				return err
+			}
+
+			if file.Name == "default.policy" {
+				defaultPolicy = policyData
+			} else {
+				customPolicies = append(customPolicies, string(policyData))
+			}
+		}
+	}
 
 	tempDir, err := os.MkdirTemp("", "policy_check")
 	if err != nil {
@@ -773,10 +807,14 @@ func downloadPolicy(log log.Component, config config.Component, _ secrets.Compon
 	}
 	defer os.RemoveAll(tempDir)
 
-	tempOutputPath := path.Join(tempDir, "check.policy")
-	if err := os.WriteFile(tempOutputPath, resBytes, 0644); err != nil {
+	if err := os.WriteFile(path.Join(tempDir, "default.policy"), defaultPolicy, 0644); err != nil {
 		return err
 	}
+	for i, customPolicy := range customPolicies {
+		if err := os.WriteFile(path.Join(tempDir, fmt.Sprintf("custom%d.policy", i+1)), []byte(customPolicy), 0644); err != nil {
+			return err
+		}
+	}
 
 	if downloadPolicyArgs.check {
 		if err := checkPolicies(log, config, &checkPoliciesCliParams{dir: tempDir}); err != nil {
@@ -784,7 +822,36 @@ func downloadPolicy(log log.Component, config config.Component, _ secrets.Compon
 		}
 	}
 
-	_, err = outputWriter.Write(resBytes)
+	// Extract and merge rules from custom policies
+	var customRules string
+	for _, customPolicy := range customPolicies {
+		customPolicyLines := strings.Split(customPolicy, "\n")
+		rulesIndex := -1
+		for i, line := range customPolicyLines {
+			if strings.TrimSpace(line) == "rules:" {
+				rulesIndex = i
+				break
+			}
+		}
+		if rulesIndex != -1 && rulesIndex+1 < len(customPolicyLines) {
+			customRules += "\n" + strings.Join(customPolicyLines[rulesIndex+1:], "\n")
+		}
+	}
+
+	// Output depending on user's specification
+	var outputContent string
+	switch downloadPolicyArgs.source {
+	case "all":
+		outputContent = string(defaultPolicy) + customRules
+	case "default":
+		outputContent = string(defaultPolicy)
+	case "custom":
+		outputContent = string(customRules)
+	default:
+		return errors.New("invalid source specified")
+	}
+
+	_, err = outputWriter.Write([]byte(outputContent))
 	if err != nil {
 		return err
 	}