diff --git a/Cargo.lock b/Cargo.lock
index d2565ecc98..df2a44a831 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2545,13 +2545,15 @@ dependencies = [
  "gitbutler-diff",
  "gitbutler-operating-modes",
  "gitbutler-oplog",
+ "gitbutler-oxidize",
  "gitbutler-project",
  "gitbutler-reference",
  "gitbutler-repo",
  "gitbutler-stack",
- "gitbutler-time",
  "gitbutler-workspace",
+ "gix",
  "serde",
+ "tracing",
 ]
 
 [[package]]
diff --git a/crates/gitbutler-edit-mode/Cargo.toml b/crates/gitbutler-edit-mode/Cargo.toml
index 1525e51983..1cb654bf77 100644
--- a/crates/gitbutler-edit-mode/Cargo.toml
+++ b/crates/gitbutler-edit-mode/Cargo.toml
@@ -7,6 +7,7 @@ publish = false
 
 [dependencies]
 git2.workspace = true
+gix.workspace = true
 anyhow.workspace = true
 bstr.workspace = true
 gitbutler-branch.workspace = true
@@ -16,11 +17,12 @@ gitbutler-command-context.workspace = true
 gitbutler-operating-modes.workspace = true
 gitbutler-project.workspace = true
 gitbutler-branch-actions.workspace = true
+gitbutler-oxidize.workspace = true
 gitbutler-reference.workspace = true
-gitbutler-time.workspace = true
 gitbutler-oplog.workspace = true
 gitbutler-diff.workspace = true
 gitbutler-stack.workspace = true
 gitbutler-cherry-pick.workspace = true
 gitbutler-workspace.workspace = true
 serde.workspace = true
+tracing.workspace = true
\ No newline at end of file
diff --git a/crates/gitbutler-edit-mode/src/lib.rs b/crates/gitbutler-edit-mode/src/lib.rs
index b7baadf29f..f228b4a70d 100644
--- a/crates/gitbutler-edit-mode/src/lib.rs
+++ b/crates/gitbutler-edit-mode/src/lib.rs
@@ -8,7 +8,7 @@ use git2::build::CheckoutBuilder;
 use gitbutler_branch_actions::internal::list_virtual_branches;
 use gitbutler_branch_actions::{update_workspace_commit, RemoteBranchFile};
 use gitbutler_cherry_pick::{ConflictedTreeKey, RepositoryExt as _};
-use gitbutler_command_context::CommandContext;
+use gitbutler_command_context::{gix_repository_for_merging, CommandContext};
 use gitbutler_commit::{
     commit_ext::CommitExt,
     commit_headers::{CommitHeadersV2, HasCommitHeaders},
@@ -18,6 +18,7 @@ use gitbutler_operating_modes::{
     operating_mode, read_edit_mode_metadata, write_edit_mode_metadata, EditModeMetadata,
     OperatingMode, EDIT_BRANCH_REF, WORKSPACE_BRANCH_REF,
 };
+use gitbutler_oxidize::{git2_to_gix_object_id, gix_to_git2_index, GixRepositoryExt};
 use gitbutler_project::access::{WorktreeReadPermission, WorktreeWritePermission};
 use gitbutler_reference::{ReferenceName, Refname};
 use gitbutler_repo::{rebase::cherry_rebase, RepositoryExt};
@@ -28,42 +29,47 @@ use serde::Serialize;
 
 pub mod commands;
 
+/// Returns an index of the the tree of `commit` if it is unconflicted, *or* produce a merged tree
+/// if `commit` is conflicted. That tree is turned into an index that records the conflicts that occurred
+/// during the merge.
 fn get_commit_index(repository: &git2::Repository, commit: &git2::Commit) -> Result<git2::Index> {
     let commit_tree = commit.tree().context("Failed to get commit's tree")?;
     // Checkout the commit as unstaged changes
     if commit.is_conflicted() {
         let base = commit_tree
             .get_name(".conflict-base-0")
-            .context("Failed to get base")?;
-        let base = repository
-            .find_tree(base.id())
-            .context("Failed to find base tree")?;
-        // Ours
+            .context("Failed to get base")?
+            .id();
         let ours = commit_tree
             .get_name(".conflict-side-0")
-            .context("Failed to get base")?;
-        let ours = repository
-            .find_tree(ours.id())
-            .context("Failed to find base tree")?;
-        // Theirs
+            .context("Failed to get base")?
+            .id();
         let theirs = commit_tree
             .get_name(".conflict-side-1")
-            .context("Failed to get base")?;
-        let theirs = repository
-            .find_tree(theirs.id())
-            .context("Failed to find base tree")?;
-
-        let index = repository
-            .merge_trees(&base, &ours, &theirs, None)
-            .context("Failed to merge trees")?;
-
-        Ok(index)
+            .context("Failed to get base")?
+            .id();
+
+        let gix_repo = gix_repository_for_merging(repository.path())?;
+        // Merge without favoring a side this time to get a tree containing the actual conflicts.
+        let mut merge_result = gix_repo.merge_trees(
+            git2_to_gix_object_id(base),
+            git2_to_gix_object_id(ours),
+            git2_to_gix_object_id(theirs),
+            gix_repo.default_merge_labels(),
+            gix_repo.tree_merge_options()?,
+        )?;
+        let merged_tree_id = merge_result.tree.write()?;
+        let mut index = gix_repo.index_from_tree(&merged_tree_id)?;
+        if !merge_result.index_changed_after_applying_conflicts(
+            &mut index,
+            gix::merge::tree::TreatAsUnresolved::git(),
+        ) {
+            tracing::warn!("There must be an issue with conflict-commit creation as re-merging the conflicting trees didn't yield a conflicting index.");
+        }
+        gix_to_git2_index(&index)
     } else {
         let mut index = git2::Index::new()?;
-        index
-            .read_tree(&commit_tree)
-            .context("Failed to set index tree")?;
-
+        index.read_tree(&commit_tree)?;
         Ok(index)
     }
 }
diff --git a/crates/gitbutler-oxidize/src/lib.rs b/crates/gitbutler-oxidize/src/lib.rs
index 2e576af2d2..18f8384826 100644
--- a/crates/gitbutler-oxidize/src/lib.rs
+++ b/crates/gitbutler-oxidize/src/lib.rs
@@ -53,3 +53,56 @@ pub fn gix_to_git2_signature(
         &time,
     )?)
 }
+
+/// Convert a `gix` index into a `git2` one.
+///
+/// Note that this is quite inefficient as it will have to re-allocate all paths.
+///
+/// ## Note
+///
+/// * Flags aren't fully supported right now, they are truncated, but good enough to get the stage right.
+///
+/// ## IMPORTANT
+///
+/// When removing this in favor of using the native `gix` index, do not forget to prune `REMOVE`d entries
+/// or otherwise handle them.
+pub fn gix_to_git2_index(index: &gix::index::State) -> anyhow::Result<git2::Index> {
+    let mut out = git2::Index::new()?;
+    for entry @ gix::index::Entry {
+        stat:
+            gix::index::entry::Stat {
+                mtime,
+                ctime,
+                dev,
+                ino,
+                uid,
+                gid,
+                size,
+            },
+        id,
+        flags,
+        mode,
+        ..
+    } in index.entries()
+    {
+        if flags.contains(gix::index::entry::Flags::REMOVE) {
+            continue;
+        }
+        let git2_entry = git2::IndexEntry {
+            ctime: git2::IndexTime::new(ctime.secs as i32, ctime.nsecs),
+            mtime: git2::IndexTime::new(mtime.secs as i32, mtime.nsecs),
+            dev: *dev,
+            ino: *ino,
+            mode: mode.bits(),
+            uid: *uid,
+            gid: *gid,
+            file_size: *size,
+            id: gix_to_git2_oid(*id),
+            flags: flags.bits() as u16,
+            flags_extended: 0,
+            path: entry.path(index).to_owned().into(),
+        };
+        out.add(&git2_entry)?
+    }
+    Ok(out)
+}