diff --git a/agent/config/builder.go b/agent/config/builder.go
index 4458f0fe71..da5f4fb2b6 100644
--- a/agent/config/builder.go
+++ b/agent/config/builder.go
@@ -79,12 +79,6 @@ type Builder struct {
 // NewBuilder returns a new configuration builder based on the given command
 // line flags.
 func NewBuilder(flags Flags) (*Builder, error) {
-	// We expect all flags to be parsed and flags.Args to be empty.
-	// Therefore, we bail if we find unparsed args.
-	if len(flags.Args) > 0 {
-		return nil, fmt.Errorf("config: Unknown extra arguments: %v", flags.Args)
-	}
-
 	newSource := func(name string, v interface{}) Source {
 		b, err := json.MarshalIndent(v, "", "    ")
 		if err != nil {
diff --git a/agent/config/flags.go b/agent/config/flags.go
index 6e0d7e31cf..739e289fa9 100644
--- a/agent/config/flags.go
+++ b/agent/config/flags.go
@@ -22,9 +22,17 @@ type Flags struct {
 
 	// HCL contains an arbitrary config in hcl format.
 	HCL []string
+}
 
-	// Args contains the remaining unparsed flags.
-	Args []string
+// ParseFlag parses the arguments into a Flags struct.
+func ParseFlags(args []string) (Flags, error) {
+	var f Flags
+	fs := flag.NewFlagSet("agent", flag.ContinueOnError)
+	AddFlags(fs, &f)
+	if err := fs.Parse(args); err != nil {
+		return Flags{}, err
+	}
+	return f, nil
 }
 
 // AddFlags adds the command line flags for the agent.
diff --git a/agent/config/flags_test.go b/agent/config/flags_test.go
index d7bb053701..87aca32cc8 100644
--- a/agent/config/flags_test.go
+++ b/agent/config/flags_test.go
@@ -1,7 +1,6 @@
 package config
 
 import (
-	"flag"
 	"reflect"
 	"strings"
 	"testing"
@@ -36,6 +35,10 @@ func TestParseFlags(t *testing.T) {
 			args:  []string{`-bootstrap=false`},
 			flags: Flags{Config: Config{Bootstrap: pBool(false)}},
 		},
+		{
+			args:  []string{`-bootstrap`, `true`},
+			flags: Flags{Config: Config{Bootstrap: pBool(true)}},
+		},
 		{
 			args:  []string{`-config-file`, `a`, `-config-dir`, `b`, `-config-file`, `c`, `-config-dir`, `d`},
 			flags: Flags{ConfigFiles: []string{"a", "b", "c", "d"}},
@@ -56,22 +59,14 @@ func TestParseFlags(t *testing.T) {
 			args:  []string{`-node-meta`, `a:b`, `-node-meta`, `c:d`},
 			flags: Flags{Config: Config{NodeMeta: map[string]string{"a": "b", "c": "d"}}},
 		},
-		{
-			args:  []string{`-bootstrap`, `true`},
-			flags: Flags{Config: Config{Bootstrap: pBool(true)}, Args: []string{"true"}},
-		},
 	}
 
 	for _, tt := range tests {
 		t.Run(strings.Join(tt.args, " "), func(t *testing.T) {
-			flags := Flags{}
-			fs := flag.NewFlagSet("", flag.ContinueOnError)
-			AddFlags(fs, &flags)
-			err := fs.Parse(tt.args)
+			flags, err := ParseFlags(tt.args)
 			if got, want := err, tt.err; !reflect.DeepEqual(got, want) {
 				t.Fatalf("got error %v want %v", got, want)
 			}
-			flags.Args = fs.Args()
 			if !verify.Values(t, "flag", flags, tt.flags) {
 				t.FailNow()
 			}
diff --git a/agent/config/runtime_test.go b/agent/config/runtime_test.go
index 9fcd608c8d..c82b959aac 100644
--- a/agent/config/runtime_test.go
+++ b/agent/config/runtime_test.go
@@ -1886,14 +1886,10 @@ func testConfig(t *testing.T, tests []configTest, dataDir string) {
 
 			t.Run(strings.Join(desc, ":"), func(t *testing.T) {
 				// first parse the flags
-				flags := Flags{}
-				fs := flag.NewFlagSet("", flag.ContinueOnError)
-				AddFlags(fs, &flags)
-				err := fs.Parse(tt.args)
+				flags, err := ParseFlags(tt.args)
 				if err != nil {
 					t.Fatalf("ParseFlags failed: %s", err)
 				}
-				flags.Args = fs.Args()
 
 				// Then create a builder with the flags.
 				b, err := NewBuilder(flags)
diff --git a/command/agent/agent.go b/command/agent/agent.go
index 2528b84fda..44c60ff722 100644
--- a/command/agent/agent.go
+++ b/command/agent/agent.go
@@ -90,7 +90,6 @@ func (c *cmd) readConfig() *config.RuntimeConfig {
 		}
 		return nil
 	}
-	c.flagArgs.Args = c.flags.Args()
 
 	b, err := config.NewBuilder(c.flagArgs)
 	if err != nil {
diff --git a/command/agent/agent_test.go b/command/agent/agent_test.go
index 8ba836f26a..7a307c3eca 100644
--- a/command/agent/agent_test.go
+++ b/command/agent/agent_test.go
@@ -31,10 +31,6 @@ func TestConfigFail(t *testing.T) {
 			args: []string{"agent", "-server", "-bind=10.0.0.1", "-datacenter="},
 			out:  "==> datacenter cannot be empty\n",
 		},
-		{
-			args: []string{"agent", "-server", "-bind=10.0.0.1", "-datacenter=foo", "some-other-arg"},
-			out:  "==> config: Unknown extra arguments: [some-other-arg]\n",
-		},
 		{
 			args: []string{"agent", "-server", "-bind=10.0.0.1"},
 			out:  "==> data_dir cannot be empty\n",