diff --git a/pkg/cli/cli.go b/pkg/cli/cli.go
index f5f71b70c26..ace342be7a8 100644
--- a/pkg/cli/cli.go
+++ b/pkg/cli/cli.go
@@ -40,6 +40,7 @@ const (
 
 	pluginsFlag        = "plugins"
 	projectVersionFlag = "project-version"
+	projectFileFlag    = "project-file"
 )
 
 // CLI is the command line utility that is used to scaffold kubebuilder project files.
@@ -73,6 +74,8 @@ type CLI struct {
 	pluginKeys []string
 	// Project version to scaffold.
 	projectVersion config.Version
+	// Project file path to use instead of default PROJECT file.
+	projectFile string
 
 	// A filtered set of plugins that should be used by command constructors.
 	resolvedPlugins []plugin.Plugin
@@ -211,6 +214,12 @@ func (c *CLI) getInfoFromConfigFile() error {
 	// Read the project configuration file
 	cfg := yamlstore.New(c.fs)
 
+	// Determine which project file to use.
+	projectPath := yamlstore.DefaultPath
+	if c.projectFile != "" {
+		projectPath = c.projectFile
+	}
+
 	// Workaround for https://github.com/kubernetes-sigs/kubebuilder/issues/4433
 	//
 	// This allows the `kubebuilder alpha generate` command to work with old projects
@@ -222,12 +231,12 @@ func (c *CLI) getInfoFromConfigFile() error {
 
 	if isAlphaGenerateCommand(os.Args[1:]) {
 		// Patch raw file bytes before unmarshalling
-		if err := patchProjectFileInMemoryIfNeeded(c.fs.FS, yamlstore.DefaultPath); err != nil {
+		if err := patchProjectFileInMemoryIfNeeded(c.fs.FS, projectPath); err != nil {
 			return err
 		}
 	}
 
-	if err := cfg.Load(); err != nil {
+	if err := cfg.LoadFrom(projectPath); err != nil {
 		return fmt.Errorf("error loading configuration: %w", err)
 	}
 
@@ -418,6 +427,13 @@ func (c *CLI) getInfoFromFlags(hasConfigFile bool) error {
 		}
 	}
 
+	// Extract the project-file flag if provided.
+	if projectFile, err := fs.GetString(projectFileFlag); err != nil {
+		return fmt.Errorf("invalid flag %q: %w", projectFileFlag, err)
+	} else if projectFile != "" {
+		c.projectFile = projectFile
+	}
+
 	return nil
 }
 
diff --git a/pkg/cli/cmd_helpers.go b/pkg/cli/cmd_helpers.go
index b6af5ef4dc9..8c6af599576 100644
--- a/pkg/cli/cmd_helpers.go
+++ b/pkg/cli/cmd_helpers.go
@@ -157,6 +157,7 @@ func (c *CLI) applySubcommandHooks(
 		store:               yamlstore.New(c.fs),
 		subcommands:         subcommands,
 		errorMessage:        errorMessage,
+		projectFile:         c.projectFile,
 		projectVersion:      c.projectVersion,
 		pluginChain:         pluginChain,
 		cliVersion:          c.cliVersion,
@@ -296,6 +297,8 @@ type executionHooksFactory struct {
 	subcommands []keySubcommandTuple
 	// errorMessage is prepended to returned errors.
 	errorMessage string
+	// projectFile is the path to the project configuration file (empty means use default: PROJECT).
+	projectFile string
 	// projectVersion is the project version that will be used to create new project configurations.
 	// It is only used for initialization.
 	projectVersion config.Version
@@ -407,7 +410,13 @@ func (factory *executionHooksFactory) preRunEFunc(
 		}
 		if createConfig {
 			// Check if a project configuration is already present.
-			if err := factory.store.Load(); err == nil || !errors.Is(err, os.ErrNotExist) {
+			var err error
+			if factory.projectFile != "" {
+				err = factory.store.LoadFrom(factory.projectFile)
+			} else {
+				err = factory.store.Load()
+			}
+			if err == nil || !errors.Is(err, os.ErrNotExist) {
 				return fmt.Errorf("%s: already initialized", factory.errorMessage)
 			}
 
@@ -417,7 +426,13 @@ func (factory *executionHooksFactory) preRunEFunc(
 			}
 		} else {
 			// Load the project configuration.
-			if err := factory.store.Load(); os.IsNotExist(err) {
+			var err error
+			if factory.projectFile != "" {
+				err = factory.store.LoadFrom(factory.projectFile)
+			} else {
+				err = factory.store.Load()
+			}
+			if os.IsNotExist(err) {
 				return fmt.Errorf("%s: failed to find configuration file, project must be initialized",
 					factory.errorMessage)
 			} else if err != nil {
@@ -507,7 +522,13 @@ func (factory *executionHooksFactory) runEFunc() func(*cobra.Command, []string)
 // and executes the post-scaffold hook.
 func (factory *executionHooksFactory) postRunEFunc() func(*cobra.Command, []string) error {
 	return func(*cobra.Command, []string) error {
-		if err := factory.store.Save(); err != nil {
+		var err error
+		if factory.projectFile != "" {
+			err = factory.store.SaveTo(factory.projectFile)
+		} else {
+			err = factory.store.Save()
+		}
+		if err != nil {
 			return fmt.Errorf("%s: failed to save configuration file: %w", factory.errorMessage, err)
 		}
 
diff --git a/pkg/cli/root.go b/pkg/cli/root.go
index b1fa1c77bc5..30f068bd28b 100644
--- a/pkg/cli/root.go
+++ b/pkg/cli/root.go
@@ -103,6 +103,7 @@ func (c CLI) newRootCmd() *cobra.Command {
 
 	// Global flags for all subcommands.
 	cmd.PersistentFlags().StringSlice(pluginsFlag, nil, "plugin keys to be used for this subcommand execution")
+	cmd.PersistentFlags().String(projectFileFlag, "", "path to the project configuration file (default \"PROJECT\")")
 
 	// Register --project-version on the root command so that it shows up in help.
 	cmd.Flags().String(projectVersionFlag, c.defaultProjectVersion.String(), "project version")