diff --git a/internal/beatcmd/cmd.go b/internal/beatcmd/cmd.go
index a312ebecdf..ddef906301 100644
--- a/internal/beatcmd/cmd.go
+++ b/internal/beatcmd/cmd.go
@@ -47,8 +47,11 @@ func NewRootCommand(beatParams BeatParams) *cobra.Command {
 	// root command is an alias for "run"
 	runCommand := genRunCmd(beatParams)
 	rootCommand := &cobra.Command{
-		Use:  "apm-server",
-		RunE: runCommand.RunE,
+		Use: "apm-server",
+		RunE: func(cmd *cobra.Command, args []string) error {
+			cfgfile.HandleFlags()
+			return runCommand.RunE(cmd, args)
+		},
 		CompletionOptions: cobra.CompletionOptions{
 			DisableDefaultCmd: true,
 		},
diff --git a/internal/beatcmd/init.go b/internal/beatcmd/init.go
index bbf657006a..5afa7b2d5c 100644
--- a/internal/beatcmd/init.go
+++ b/internal/beatcmd/init.go
@@ -19,12 +19,9 @@ package beatcmd
 
 import (
 	cryptorand "crypto/rand"
-	"log"
 	"math"
 	"math/big"
 	"math/rand"
-	"os"
-	"strings"
 	"time"
 
 	"github.com/elastic/beats/v7/libbeat/cfgfile"
@@ -55,14 +52,11 @@ func initRand() {
 }
 
 func initFlags() {
-	// For backwards compatibility, convert -flags to --flags.
-	for i, arg := range os.Args[1:] {
-		if strings.HasPrefix(arg, "-") && !strings.HasPrefix(arg, "--") && len(arg) > 2 {
-			os.Args[1+i] = "-" + arg
-		}
-	}
-
-	if err := cfgfile.HandleFlags(); err != nil {
-		log.Fatal(err)
-	}
+	// For backwards compatibility, initialize and convert known -flags to --flags.
+	cfgfile.Initialize()
+	cfgfile.AddAllowedBackwardsCompatibleFlag("v")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("e")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("d")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("environment")
+	cfgfile.ConvertFlagsForBackwardsCompatibility()
 }