diff --git a/agent/config/builder.go b/agent/config/builder.go
index da5f4fb2b6..4458f0fe71 100644
--- a/agent/config/builder.go
+++ b/agent/config/builder.go
@@ -79,6 +79,12 @@ 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 739e289fa9..6e0d7e31cf 100644
--- a/agent/config/flags.go
+++ b/agent/config/flags.go
@@ -22,17 +22,9 @@ type Flags struct {
 
 	// HCL contains an arbitrary config in hcl format.
 	HCL []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
+	// Args contains the remaining unparsed flags.
+	Args []string
 }
 
 // AddFlags adds the command line flags for the agent.
diff --git a/agent/config/flags_test.go b/agent/config/flags_test.go
index 87aca32cc8..d7bb053701 100644
--- a/agent/config/flags_test.go
+++ b/agent/config/flags_test.go
@@ -1,6 +1,7 @@
 package config
 
 import (
+	"flag"
 	"reflect"
 	"strings"
 	"testing"
@@ -35,10 +36,6 @@ 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"}},
@@ -59,14 +56,22 @@ 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, err := ParseFlags(tt.args)
+			flags := Flags{}
+			fs := flag.NewFlagSet("", flag.ContinueOnError)
+			AddFlags(fs, &flags)
+			err := fs.Parse(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 c82b959aac..9fcd608c8d 100644
--- a/agent/config/runtime_test.go
+++ b/agent/config/runtime_test.go
@@ -1886,10 +1886,14 @@ func testConfig(t *testing.T, tests []configTest, dataDir string) {
 
 			t.Run(strings.Join(desc, ":"), func(t *testing.T) {
 				// first parse the flags
-				flags, err := ParseFlags(tt.args)
+				flags := Flags{}
+				fs := flag.NewFlagSet("", flag.ContinueOnError)
+				AddFlags(fs, &flags)
+				err := fs.Parse(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 44c60ff722..2528b84fda 100644
--- a/command/agent/agent.go
+++ b/command/agent/agent.go
@@ -90,6 +90,7 @@ 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 7a307c3eca..8ba836f26a 100644
--- a/command/agent/agent_test.go
+++ b/command/agent/agent_test.go
@@ -31,6 +31,10 @@ 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",