diff --git a/cli/command/cli.go b/cli/command/cli.go
index a9e7e30763..7b5048e98f 100644
--- a/cli/command/cli.go
+++ b/cli/command/cli.go
@@ -308,9 +308,9 @@ func newAPIClientFromEndpoint(ep docker.Endpoint, configFile *configfile.ConfigF
 	if err != nil {
 		return nil, err
 	}
-	customHeaders := configFile.HTTPHeaders
-	if customHeaders == nil {
-		customHeaders = map[string]string{}
+	customHeaders := make(map[string]string, len(configFile.HTTPHeaders))
+	for k, v := range configFile.HTTPHeaders {
+		customHeaders[k] = v
 	}
 	customHeaders["User-Agent"] = UserAgent()
 	clientOpts = append(clientOpts, client.WithHTTPHeaders(customHeaders))
diff --git a/cli/command/cli_test.go b/cli/command/cli_test.go
index 32c999df75..83f42e9df0 100644
--- a/cli/command/cli_test.go
+++ b/cli/command/cli_test.go
@@ -45,6 +45,7 @@ func TestNewAPIClientFromFlags(t *testing.T) {
 	}
 	assert.Check(t, is.DeepEqual(expectedHeaders, apiclient.(*client.Client).CustomHTTPHeaders()))
 	assert.Check(t, is.Equal(api.DefaultVersion, apiclient.ClientVersion()))
+	assert.DeepEqual(t, configFile.HTTPHeaders, map[string]string{"My-Header": "Custom-Value"})
 }
 
 func TestNewAPIClientFromFlagsForDefaultSchema(t *testing.T) {