diff --git a/apps/desktop/src/lib/backend/projects.ts b/apps/desktop/src/lib/backend/projects.ts
index 29669657d9..83bdd59e42 100644
--- a/apps/desktop/src/lib/backend/projects.ts
+++ b/apps/desktop/src/lib/backend/projects.ts
@@ -28,6 +28,7 @@ export class Project {
 	use_diff_context: boolean | undefined;
 	snapshot_lines_threshold!: number | undefined;
 	use_new_branch_integration_algorithm: boolean | undefined;
+	use_new_integration_check!: boolean;
 	// Produced just for the frontend to determine if the project is open in any window.
 	is_open!: boolean;
 
diff --git a/apps/desktop/src/lib/settings/userPreferences/PreferencesForm.svelte b/apps/desktop/src/lib/settings/userPreferences/PreferencesForm.svelte
index 107f5975fc..1b81cbf60b 100644
--- a/apps/desktop/src/lib/settings/userPreferences/PreferencesForm.svelte
+++ b/apps/desktop/src/lib/settings/userPreferences/PreferencesForm.svelte
@@ -1,5 +1,5 @@
 <script lang="ts">
-	import { Project, ProjectsService } from '$lib/backend/projects';
+	import { Project, ProjectService, ProjectsService } from '$lib/backend/projects';
 	import { projectRunCommitHooks } from '$lib/config/config';
 	import Section from '$lib/settings/Section.svelte';
 	import { getContext } from '@gitbutler/shared/context';
@@ -8,7 +8,9 @@
 	import Toggle from '@gitbutler/ui/Toggle.svelte';
 
 	const projectsService = getContext(ProjectsService);
+	const projectService = getContext(ProjectService);
 	const project = getContext(Project);
+	const projectStore = projectService.project;
 
 	let snaphotLinesThreshold = project?.snapshot_lines_threshold || 20; // when undefined, the default is 20
 	let omitCertificateCheck = project?.omit_certificate_check;
@@ -16,6 +18,13 @@
 
 	const runCommitHooks = projectRunCommitHooks(project.id);
 
+	function toggleUseNewIntegrationCheck() {
+		const updatedProject = structuredClone($projectStore);
+		if (!updatedProject) return;
+		updatedProject.use_new_integration_check = !updatedProject.use_new_integration_check;
+		projectsService.updateProject(updatedProject);
+	}
+
 	async function setOmitCertificateCheck(value: boolean | undefined) {
 		project.omit_certificate_check = !!value;
 		await projectsService.updateProject(project);
@@ -112,4 +121,18 @@
 			/>
 		{/snippet}
 	</SectionCard>
+
+	<SectionCard labelFor="newIntegrationAlgorithm" orientation="row">
+		{#snippet title()}New Integration Algorithm{/snippet}
+		{#snippet caption()}
+			A new algorithm for finding integrated commits
+		{/snippet}
+		{#snippet actions()}
+			<Toggle
+				id="newIntegrationAlgorithm"
+				checked={$projectStore?.use_new_integration_check}
+				onclick={toggleUseNewIntegrationCheck}
+			/>
+		{/snippet}
+	</SectionCard>
 </Section>
diff --git a/crates/gitbutler-branch-actions/src/integration_check.rs b/crates/gitbutler-branch-actions/src/integration_check.rs
index 04d365d974..2bf7a86064 100644
--- a/crates/gitbutler-branch-actions/src/integration_check.rs
+++ b/crates/gitbutler-branch-actions/src/integration_check.rs
@@ -7,6 +7,7 @@ use gitbutler_commit::commit_ext::CommitExt as _;
 use gitbutler_oxidize::{git2_to_gix_object_id, GixRepositoryExt as _, ObjectIdExt as _, OidExt};
 use gitbutler_repo::{signature, GixRepositoryExt};
 use itertools::Itertools as _;
+use tracing::instrument;
 
 use crate::commit_ops::{get_exclusive_tree, get_first_parent, is_subset, SubsetKind};
 
@@ -103,6 +104,12 @@ fn find_related_commits(
     let mut relations: Vec<CommitRelation> = vec![];
 
     for left in lefts {
+        // Ignore conflicted commits
+        let left_commit = repository.find_commit(*left)?;
+        if left_commit.is_conflicted() {
+            continue;
+        }
+
         // First identify the list of commits on the RHS which are supersets
         // or equal to the current `left` commit.
         let mut found_supersets: Vec<CommitRelation> = vec![];
@@ -313,6 +320,10 @@ impl<'repo, 'cache, 'graph> IsCommitIntegrated<'repo, 'cache, 'graph> {
 impl IsCommitIntegrated<'_, '_, '_> {
     #[deprecated]
     fn is_integrated(&mut self, commit: &git2::Commit<'_>) -> Result<bool> {
+        if commit.is_conflicted() {
+            return Ok(false);
+        }
+
         if self.target_commit_id == git2_to_gix_object_id(commit.id()) {
             // could not be integrated if heads are the same.
             return Ok(false);
@@ -377,6 +388,7 @@ impl IsCommitIntegrated<'_, '_, '_> {
 
 /// Used to switch between the old and new algorithms. We will be able to
 /// get rid of all of this when we are confident in the new algorithm.
+#[instrument(skip(gix_repository, repository, graph))]
 pub(crate) fn compat_find_integrated_commits<'repo>(
     gix_repository: &'repo gix::Repository,
     repository: &'repo git2::Repository,
diff --git a/crates/gitbutler-project/src/storage.rs b/crates/gitbutler-project/src/storage.rs
index 2341b39411..e30b7876ee 100644
--- a/crates/gitbutler-project/src/storage.rs
+++ b/crates/gitbutler-project/src/storage.rs
@@ -28,6 +28,7 @@ pub struct UpdateRequest {
     pub use_diff_context: Option<bool>,
     pub snapshot_lines_threshold: Option<usize>,
     pub use_new_branch_integration_algorithm: Option<bool>,
+    pub use_new_integration_check: Option<bool>,
 }
 
 impl Storage {
@@ -130,6 +131,10 @@ impl Storage {
             project.use_new_branch_integration_algorithm = Some(new_branch_integration_algorithm);
         }
 
+        if let Some(use_new_integration_check) = update_request.use_new_integration_check {
+            project.use_new_integration_check = use_new_integration_check;
+        }
+
         self.inner
             .write(PROJECTS_FILE, &serde_json::to_string_pretty(&projects)?)?;