diff --git a/libbeat/cfgfile/cfgfile.go b/libbeat/cfgfile/cfgfile.go
index 21d052d64da2..f77325109779 100644
--- a/libbeat/cfgfile/cfgfile.go
+++ b/libbeat/cfgfile/cfgfile.go
@@ -22,6 +22,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"sync"
 
 	"github.com/elastic/beats/v7/libbeat/common"
 	"github.com/elastic/beats/v7/libbeat/common/fleetmode"
@@ -34,8 +35,10 @@ var (
 	// The default config cannot include the beat name as it is not initialized
 	// when this variable is created. See ChangeDefaultCfgfileFlag which should
 	// be called prior to flags.Parse().
-	configfiles = config.StringArrFlag(nil, "c", "beat.yml", "Configuration file, relative to path.config")
-	overwrites  = config.SettingFlag(nil, "E", "Configuration overwrite")
+	commandLine     flag.FlagSet
+	commandLineOnce sync.Once
+	configfiles     = config.StringArrFlag(&commandLine, "c", "beat.yml", "Configuration file, relative to path.config")
+	overwrites      = config.SettingFlag(&commandLine, "E", "Configuration overwrite")
 
 	// Additional default settings, that must be available for variable expansion
 	defaults = config.MustNewConfigFrom(map[string]interface{}{
@@ -55,7 +58,7 @@ var (
 func init() {
 	// add '-path.x' options overwriting paths in 'overwrites' config
 	makePathFlag := func(name, usage string) *string {
-		return config.ConfigOverwriteFlag(nil, overwrites, name, name, "", usage)
+		return config.ConfigOverwriteFlag(&commandLine, overwrites, name, name, "", usage)
 	}
 
 	homePath = makePathFlag("path.home", "Home path")
@@ -64,6 +67,17 @@ func init() {
 	makePathFlag("path.logs", "Logs path")
 }
 
+// InitFlags is for explicitly initializing the flags.
+// It may get called repeatedly for different flagsets, but not
+// twice for the same one.
+func InitFlags() {
+	commandLineOnce.Do(func() {
+		commandLine.VisitAll(func(f *flag.Flag) {
+			flag.CommandLine.Var(f.Value, f.Name, f.Usage)
+		})
+	})
+}
+
 // OverrideChecker checks if a config should be overwritten.
 type OverrideChecker func(*config.C) bool
 
diff --git a/libbeat/cmd/instance/beat_integration_test.go b/libbeat/cmd/instance/beat_integration_test.go
index a3388399e76a..4c2aa94bd1d4 100644
--- a/libbeat/cmd/instance/beat_integration_test.go
+++ b/libbeat/cmd/instance/beat_integration_test.go
@@ -18,6 +18,7 @@
 package instance_test
 
 import (
+	"context"
 	"encoding/json"
 	"flag"
 	"net/http"
@@ -26,6 +27,7 @@ import (
 	"time"
 
 	"github.com/elastic/beats/v7/libbeat/beat"
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/mock"
 	"github.com/elastic/elastic-agent-libs/config"
@@ -77,6 +79,7 @@ func (mb mockbeat) Stop() {
 }
 
 func TestMonitoringNameFromConfig(t *testing.T) {
+
 	mockBeat := mockbeat{
 		done:     make(chan struct{}),
 		initDone: make(chan struct{}),
@@ -90,9 +93,11 @@ func TestMonitoringNameFromConfig(t *testing.T) {
 	go func() {
 		defer wg.Done()
 
+		// Initialize cfgfile flags
+		cfgfile.InitFlags()
 		// Set the configuration file path flag so the beat can read it
-		flag.Set("c", "testdata/mockbeat.yml")
-		instance.Run(mock.Settings, func(_ *beat.Beat, _ *config.C) (beat.Beater, error) {
+		_ = flag.Set("c", "testdata/mockbeat.yml")
+		_ = instance.Run(mock.Settings, func(_ *beat.Beat, _ *config.C) (beat.Beater, error) {
 			return &mockBeat, nil
 		})
 	}()
@@ -109,9 +114,13 @@ func TestMonitoringNameFromConfig(t *testing.T) {
 	// the HTTP server goroutine
 	time.Sleep(10 * time.Millisecond)
 
-	resp, err := http.Get("http://localhost:5066/state")
+	req, err := http.NewRequestWithContext(context.Background(), http.MethodGet, "http://localhost:5066/state", nil)
+	if err != nil {
+		t.Fatalf("error creating request: %v", err)
+	}
+	resp, err := http.DefaultClient.Do(req)
 	if err != nil {
-		t.Fatal("calling state endpoint: ", err.Error())
+		t.Fatalf("calling state endpoint: %v", err)
 	}
 	defer resp.Body.Close()
 
diff --git a/libbeat/cmd/root.go b/libbeat/cmd/root.go
index be2cb9d441ae..671b72fde1ec 100644
--- a/libbeat/cmd/root.go
+++ b/libbeat/cmd/root.go
@@ -61,7 +61,7 @@ type BeatsRootCmd struct {
 func GenRootCmdWithSettings(beatCreator beat.Creator, settings instance.Settings) *BeatsRootCmd {
 	// Add global Elasticsearch license endpoint check.
 	// Check we are actually talking with Elasticsearch, to ensure that used features actually exist.
-	elasticsearch.RegisterGlobalCallback(licenser.FetchAndVerify)
+	_, _ = elasticsearch.RegisterGlobalCallback(licenser.FetchAndVerify)
 
 	if err := platformcheck.CheckNativePlatformCompat(); err != nil {
 		fmt.Fprintf(os.Stderr, "Failed to initialize: %v\n", err)
@@ -78,9 +78,12 @@ func GenRootCmdWithSettings(beatCreator beat.Creator, settings instance.Settings
 	// Due to a dependence upon the beat name, the default config file path
 	err := cfgfile.ChangeDefaultCfgfileFlag(settings.Name)
 	if err != nil {
-		panic(fmt.Errorf("failed to set default config file path: %v", err))
+		panic(fmt.Errorf("failed to set default config file path: %w", err))
 	}
 
+	// Initialize the configuration flags.
+	cfgfile.InitFlags()
+
 	// must be updated prior to CLI flag handling.
 
 	rootCmd.RunCmd = genRunCmd(settings, beatCreator)