diff --git a/bundle/run/options.go b/bundle/run/options.go
index 580612d0ea..4e50788a9b 100644
--- a/bundle/run/options.go
+++ b/bundle/run/options.go
@@ -12,15 +12,19 @@ type Options struct {
 }
 
 func (o *Options) Define(cmd *cobra.Command) {
-	wrappedCmd := cmdgroup.NewCommandWithGroupFlag(cmd)
-	jobGroup := wrappedCmd.AddFlagGroup("Job")
+	jobGroup := cmdgroup.NewFlagGroup("Job")
 	o.Job.DefineJobOptions(jobGroup.FlagSet())
 
-	jobTaskGroup := wrappedCmd.AddFlagGroup("Job Task")
+	jobTaskGroup := cmdgroup.NewFlagGroup("Job Task")
 	jobTaskGroup.SetDescription(`Note: please prefer use of job-level parameters (--param) over task-level parameters.
   For more information, see https://docs.databricks.com/en/workflows/jobs/create-run-jobs.html#pass-parameters-to-a-databricks-job-task`)
 	o.Job.DefineTaskOptions(jobTaskGroup.FlagSet())
 
-	pipelineGroup := wrappedCmd.AddFlagGroup("Pipeline")
+	pipelineGroup := cmdgroup.NewFlagGroup("Pipeline")
 	o.Pipeline.Define(pipelineGroup.FlagSet())
+
+	wrappedCmd := cmdgroup.NewCommandWithGroupFlag(cmd)
+	wrappedCmd.AddFlagGroup(jobGroup)
+	wrappedCmd.AddFlagGroup(jobTaskGroup)
+	wrappedCmd.AddFlagGroup(pipelineGroup)
 }
diff --git a/libs/cmdgroup/command.go b/libs/cmdgroup/command.go
index 19c9af16af..a2a776935d 100644
--- a/libs/cmdgroup/command.go
+++ b/libs/cmdgroup/command.go
@@ -23,6 +23,24 @@ func (c *CommandWithGroupFlag) FlagGroups() []*FlagGroup {
 	return c.flagGroups
 }
 
+func (c *CommandWithGroupFlag) NonGroupedFlags() *pflag.FlagSet {
+	nonGrouped := pflag.NewFlagSet("non-grouped", pflag.ContinueOnError)
+	c.cmd.LocalFlags().VisitAll(func(f *pflag.Flag) {
+		for _, fg := range c.flagGroups {
+			if fg.Has(f) {
+				return
+			}
+		}
+		nonGrouped.AddFlag(f)
+	})
+
+	return nonGrouped
+}
+
+func (c *CommandWithGroupFlag) HasNonGroupedFlags() bool {
+	return c.NonGroupedFlags().HasFlags()
+}
+
 func NewCommandWithGroupFlag(cmd *cobra.Command) *CommandWithGroupFlag {
 	cmdWithFlagGroups := &CommandWithGroupFlag{cmd: cmd, flagGroups: make([]*FlagGroup, 0)}
 	cmd.SetUsageFunc(func(c *cobra.Command) error {
@@ -36,10 +54,9 @@ func NewCommandWithGroupFlag(cmd *cobra.Command) *CommandWithGroupFlag {
 	return cmdWithFlagGroups
 }
 
-func (c *CommandWithGroupFlag) AddFlagGroup(name string) *FlagGroup {
-	fg := &FlagGroup{name: name, flagSet: pflag.NewFlagSet(name, pflag.ContinueOnError)}
+func (c *CommandWithGroupFlag) AddFlagGroup(fg *FlagGroup) {
 	c.flagGroups = append(c.flagGroups, fg)
-	return fg
+	c.cmd.Flags().AddFlagSet(fg.FlagSet())
 }
 
 type FlagGroup struct {
@@ -48,6 +65,10 @@ type FlagGroup struct {
 	flagSet     *pflag.FlagSet
 }
 
+func NewFlagGroup(name string) *FlagGroup {
+	return &FlagGroup{name: name, flagSet: pflag.NewFlagSet(name, pflag.ContinueOnError)}
+}
+
 func (c *FlagGroup) Name() string {
 	return c.name
 }
@@ -64,6 +85,10 @@ func (c *FlagGroup) FlagSet() *pflag.FlagSet {
 	return c.flagSet
 }
 
+func (c *FlagGroup) Has(f *pflag.Flag) bool {
+	return c.flagSet.Lookup(f.Name) != nil
+}
+
 var templateFuncs = template.FuncMap{
 	"trim":                    strings.TrimSpace,
 	"trimRightSpace":          trimRightSpace,
diff --git a/libs/cmdgroup/command_test.go b/libs/cmdgroup/command_test.go
index 2eae31d14e..9122c78090 100644
--- a/libs/cmdgroup/command_test.go
+++ b/libs/cmdgroup/command_test.go
@@ -18,15 +18,17 @@ func TestCommandFlagGrouping(t *testing.T) {
 	}
 
 	wrappedCmd := NewCommandWithGroupFlag(cmd)
-	jobGroup := wrappedCmd.AddFlagGroup("Job")
+	jobGroup := NewFlagGroup("Job")
 	fs := jobGroup.FlagSet()
 	fs.String("job-name", "", "Name of the job")
 	fs.String("job-type", "", "Type of the job")
+	wrappedCmd.AddFlagGroup(jobGroup)
 
-	pipelineGroup := wrappedCmd.AddFlagGroup("Pipeline")
+	pipelineGroup := NewFlagGroup("Pipeline")
 	fs = pipelineGroup.FlagSet()
 	fs.String("pipeline-name", "", "Name of the pipeline")
 	fs.String("pipeline-type", "", "Type of the pipeline")
+	wrappedCmd.AddFlagGroup(pipelineGroup)
 
 	cmd.Flags().BoolP("bool", "b", false, "Bool flag")
 
@@ -48,4 +50,10 @@ Pipeline Flags:
 Flags:
   -b, --bool   Bool flag`
 	require.Equal(t, expected, buf.String())
+
+	require.NotNil(t, cmd.Flags().Lookup("job-name"))
+	require.NotNil(t, cmd.Flags().Lookup("job-type"))
+	require.NotNil(t, cmd.Flags().Lookup("pipeline-name"))
+	require.NotNil(t, cmd.Flags().Lookup("pipeline-type"))
+	require.NotNil(t, cmd.Flags().Lookup("bool"))
 }
diff --git a/libs/cmdgroup/template.go b/libs/cmdgroup/template.go
index aac967b0ee..5c1be48fb4 100644
--- a/libs/cmdgroup/template.go
+++ b/libs/cmdgroup/template.go
@@ -7,8 +7,8 @@ const usageTemplate = `Usage:{{if .Command.Runnable}}
   {{.Description}}{{end}}
 {{.FlagSet.FlagUsages | trimTrailingWhitespaces}}
 {{end}}
-{{if .Command.HasAvailableLocalFlags}}Flags:
-{{.Command.LocalFlags.FlagUsages | trimTrailingWhitespaces}}{{end}}{{if .Command.HasAvailableInheritedFlags}}
+{{if .HasNonGroupedFlags}}Flags:
+{{.NonGroupedFlags.FlagUsages | trimTrailingWhitespaces}}{{end}}{{if .Command.HasAvailableInheritedFlags}}
 
 Global Flags:
 {{.Command.InheritedFlags.FlagUsages | trimTrailingWhitespaces}}{{end}}`