GitHub · Pull requests · Merging · Checked October 27, 2026

GitHub: the next pull request shows commits that were already squash merged

Squash and merge combines the commits of a pull request into one commit on the base branch; the intermediate commits from the pull request are not preserved as separate commits there. If you keep working on the same head branch after a squash merge, later pull requests can include commits that were already squashed into the base branch, which makes merge conflicts more likely and can force you to resolve the same conflicts more than once (GitHub's squashing and merging a long-running branch, checked October 27, 2026).

feature: A - B - C           squash merged as S on main
main:    ... - S
feature: A - B - C - D       next pull request can include A, B and C again

Why the old commits come back

A new commit on the base branch: the squash commit is a new commit, and the commits of the pull request are not preserved as separate commits on the base branch (GitHub's squash and merge your commits).
The diff starts at the merge base: pull requests on GitHub show a three-dot diff, from the most recent common commit of both branches to the newest version of the topic branch, so it keeps showing what the branch introduced since the branches diverged (GitHub's three-dot and two-dot comparisons). See compare refused for the comparison itself.
Conflicts again: GitHub says this makes merge conflicts more likely and can force you to resolve the same conflicts more than once (see merge conflicts).

What to do

Start from the base branch: GitHub says squash merging works best for short-lived branches, so start the next change from the updated base branch rather than from the merged branch.
A long-running branch: GitHub suggests a merge commit for it, or rebasing the branch before opening the next pull request.
Merge the base often: merging the base branch into the topic branch frequently makes the two-dot and three-dot diffs the same, and GitHub recommends merging pull requests as soon as possible (GitHub's merging often).
Delete the branch after the merge: the repository setting Automatically delete head branches, or deleting it by hand, keeps a merged branch from being reused (see branch not deleted after merging).
Choose the method on purpose: the repository decides which methods are allowed and the default squash commit message (see merge method not allowed).

GitHub pull requests in IntelliJ IDEA

Pull Request Inbox for GitHub, a plugin by Lesstep for JetBrains IDEs 2024.1 or later, shows a pull request's diff from the merge base, as GitHub does, next to its reviews, checks and conversations, and merges it with the methods the target branch allows. Its merge dialog can delete the head branch after merging, and follows the repository setting Automatically delete head branches when it can read it. The review inbox, diffs and conversations are free; approving, commenting, resolving and merging are Pro (US$1.50 a month, with a 30-day trial).

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