diff --git a/docs/book/src/reference/commands/alpha_update.md b/docs/book/src/reference/commands/alpha_update.md
index 3d937794508..017bd57efda 100644
--- a/docs/book/src/reference/commands/alpha_update.md
+++ b/docs/book/src/reference/commands/alpha_update.md
@@ -61,6 +61,12 @@ kubebuilder alpha update \
   --from-branch=main
 ```
 
+Force update even with merge conflicts:
+
+```sh
+kubebuilder alpha update --force
+```
+
 <aside class="note warning">
 <h1>You might need to upgrade your project first</h1>
 
@@ -81,17 +87,58 @@ Once updated, you can use `kubebuilder alpha update` for future upgrades.
 | `--from-version`    | **Required for projects initialized with versions earlier than v4.6.0.** Kubebuilder version your project was created with. If unset, uses the `PROJECT` file. |
 | `--to-version`      | Version to upgrade to. Defaults to the latest version.                                                                                                         |
 | `--from-branch`     | Git branch that contains your current project code. Defaults to `main`.                                                                                        |
+| `--force`           | Force the update even if conflicts occur. Conflicted files will include conflict markers, and a commit will be created automatically. Ideal for automation (e.g., cronjobs, CI).                                                                       |
 | `-h, --help`        | Show help for this command.                                                                                                                                    |
-
-<aside class="note warning">
-<h1>Projects generated with </h1>
-
+<aside class="note">
 Projects generated with **Kubebuilder v4.6.0** or later include the `cliVersion` field in the `PROJECT` file.
 This field is used by `kubebuilder alpha update` to determine the correct CLI
 version for upgrading your project.
+</aside>
+
+## Merge Conflicts with `--force`
+
+When you use the `--force` flag with `kubebuilder alpha update`, Git will complete the merge even if there are conflicts. The resulting commit will include conflict markers like:
+```
+<<<<<<< HEAD
+Your changes
+=======
+Incoming changes
+>>>>>>> branch-name
+```
+These conflicts will be committed in the
+`tmp-kb-update-merge` branch.
 
+<aside class="note warning">
+You must manually resolve these conflicts before merging into your main branch.
+
+```suggestion
+<aside class="note warning">
+<H1>If you face conflicts (using or not the --force flag) </H1>
+If the merge introduces conflicts, you must resolve them and **ensure** you execute the following command to regenerate the manifests and organise the files properly:
+
+```bash
+make manifests generate fmt vet lint-fix
+```
+
+Alternatively, you may want to run:
+
+```bash
+make all
+```
 </aside>
 
+
+## When to Use `--force`
+Use `--force` only in scenarios like:
+- Automated environments (e.g., CI pipelines or cron jobs)
+- When you need to create a PR even if conflicts are present
+- When a human will resolve the conflicts later
+`kubebuilder alpha update --force`
+
+This ensures the update proceeds without manual blocking but shifts responsibility for conflict resolution to a follow-up manual step.
+
+This approach is typically used in automation workflows where conflict markers are later addressed by a human, or where preserving the conflicting changes is acceptable for follow-up processing.
+
 ## Requirements
 
 - A valid [PROJECT][project-config] file at the root of your project
diff --git a/pkg/cli/alpha/internal/update/update.go b/pkg/cli/alpha/internal/update/update.go
index 9d9275cbab2..212bc333b6d 100644
--- a/pkg/cli/alpha/internal/update/update.go
+++ b/pkg/cli/alpha/internal/update/update.go
@@ -39,6 +39,8 @@ type Update struct {
 	ToVersion string
 	// FromBranch stores the branch to update from, e.g., "main".
 	FromBranch string
+	// Force commits the update changes even with merge conflicts
+	Force bool
 
 	// UpdateBranches
 	AncestorBranch string
@@ -335,8 +337,15 @@ func (opts *Update) mergeOriginalToUpgrade() error {
 		var exitErr *exec.ExitError
 		// If the merge has an error that is not a conflict, return an error 2
 		if errors.As(err, &exitErr) && exitErr.ExitCode() == 1 {
-			log.Warn("Merge completed with conflicts. Manual resolution required.")
 			hasConflicts = true
+			if !opts.Force {
+				log.Warn("Merge stopped due to conflicts. Manual resolution is required.")
+				log.Warn("After resolving the conflicts, run the following command:")
+				log.Warn("    make manifests generate fmt vet lint-fix")
+				log.Warn("This ensures manifests and generated files are up to date, and the project layout remains consistent.")
+				return fmt.Errorf("merge stopped due to conflicts")
+			}
+			log.Warn("Merge completed with conflicts. Conflict markers will be committed.")
 		} else {
 			return fmt.Errorf("merge failed unexpectedly: %w", err)
 		}
diff --git a/pkg/cli/alpha/update.go b/pkg/cli/alpha/update.go
index 8e61762db4e..f0211163616 100644
--- a/pkg/cli/alpha/update.go
+++ b/pkg/cli/alpha/update.go
@@ -50,9 +50,8 @@ The process uses Git branches:
   - upgrade: scaffold from the target version
   - merge: result of the 3-way merge
 
-If conflicts occur during the merge, resolve them manually in the 'merge' branch. 
-Once resolved, commit and push it as a pull request. This branch will contain the 
-final upgraded project with the latest Kubebuilder layout and your custom code.
+If conflicts occur during the merge, the command will stop and leave the merge branch for manual resolution.
+Use --force to commit conflicts with markers instead. 
 
 Examples:
   # Update from the version specified in the PROJECT file to the latest release
@@ -64,6 +63,9 @@ Examples:
   # Update from a specific version to an specific release
   kubebuilder alpha update --from-version v4.5.0 --to-version v4.7.0	
 
+  # Force update even with merge conflicts (commit conflict markers)
+  kubebuilder alpha update --force
+
 `,
 
 		PreRunE: func(_ *cobra.Command, _ []string) error {
@@ -93,5 +95,9 @@ Examples:
 	updateCmd.Flags().StringVar(&opts.FromBranch, "from-branch", "",
 		"Git branch to use as current state of the project for the update.")
 
+	updateCmd.Flags().BoolVar(&opts.Force, "force", false,
+		"Force the update even if conflicts occur. Conflicted files will include conflict markers, and a "+
+			"commit will be created automatically. Ideal for automation (e.g., cronjobs, CI).")
+
 	return updateCmd
 }