diff --git a/src/github/pullRequestGitHelper.ts b/src/github/pullRequestGitHelper.ts
index 6d93d2b176..343377ded0 100644
--- a/src/github/pullRequestGitHelper.ts
+++ b/src/github/pullRequestGitHelper.ts
@@ -307,6 +307,17 @@ export class PullRequestGitHelper {
 		return `${owner}#${repository}#${baseBranch}`;
 	}
 
+	private static async setConfig(repository: Repository, key: string, value: string): Promise<void> {
+		const existingConfigs = (await repository.getConfigs()).filter(config => config.key === key);
+		if (existingConfigs.some(config => config.value === value)) {
+			return;
+		}
+		if (existingConfigs.length === 1 && repository.unsetConfig) {
+			await repository.unsetConfig(key);
+		}
+		await repository.setConfig(key, value);
+	}
+
 	static parsePullRequestMetadata(value: string): PullRequestMetadata | undefined {
 		if (value) {
 			const matches = /(.*)#(.*)#(.*)/g.exec(value);
@@ -434,7 +445,7 @@ export class PullRequestGitHelper {
 			}
 			const prConfigKey = `branch.${branchName}.${PullRequestMetadataKey}`;
 			if (pullRequest) {
-				await repository.setConfig(prConfigKey, PullRequestGitHelper.buildPullRequestMetadata(pullRequest));
+				await PullRequestGitHelper.setConfig(repository, prConfigKey, PullRequestGitHelper.buildPullRequestMetadata(pullRequest));
 			} else if (repository.unsetConfig) {
 				await repository.unsetConfig(prConfigKey);
 			}
@@ -458,7 +469,7 @@ export class PullRequestGitHelper {
 			const prConfigKey = `branch.${branch}.${BaseBranchMetadataKey}`;
 			if (base) {
 				Logger.appendLine(`associate ${branch} with base branch ${base.owner}/${base.repo}#${base.branch}`, PullRequestGitHelper.ID);
-				await repository.setConfig(prConfigKey, PullRequestGitHelper.buildBaseBranchMetadata(base.owner, base.repo, base.branch));
+				await PullRequestGitHelper.setConfig(repository, prConfigKey, PullRequestGitHelper.buildBaseBranchMetadata(base.owner, base.repo, base.branch));
 			} else if (repository.unsetConfig) {
 				await repository.unsetConfig(prConfigKey);
 				const vscodeBaseBranchConfigKey = `branch.${branch}.${VscodeBaseBranchMetadataKey}`;
diff --git a/src/test/github/pullRequestGitHelper.test.ts b/src/test/github/pullRequestGitHelper.test.ts
index 8c51164df0..9c50b09e11 100644
--- a/src/test/github/pullRequestGitHelper.test.ts
+++ b/src/test/github/pullRequestGitHelper.test.ts
@@ -189,6 +189,52 @@ describe('PullRequestGitHelper', function () {
 		});
 	});
 
+	describe('associateBranchWithPullRequest', function () {
+		const pullRequest = (number: number) => ({
+			number,
+			base: {
+				repositoryCloneUrl: {
+					owner: 'owner',
+					repositoryName: 'name',
+				},
+			},
+		}) as PullRequestModel;
+
+		it('replaces pull request metadata instead of appending values', async function () {
+			await PullRequestGitHelper.associateBranchWithPullRequest(repository, pullRequest(100), 'feature');
+			await PullRequestGitHelper.associateBranchWithPullRequest(repository, pullRequest(100), 'feature');
+			await PullRequestGitHelper.associateBranchWithPullRequest(repository, pullRequest(101), 'feature');
+
+			const key = 'branch.feature.github-pr-owner-number';
+			assert.deepStrictEqual((await repository.getConfigs()).filter(config => config.key === key), [
+				{ key, value: 'owner#name#101' },
+			]);
+		});
+
+		it('does not append to existing duplicate metadata', async function () {
+			const key = 'branch.feature.github-pr-owner-number';
+			await repository.setConfig(key, 'owner#name#100');
+			await repository.setConfig(key, 'owner#name#100');
+
+			await PullRequestGitHelper.associateBranchWithPullRequest(repository, pullRequest(100), 'feature');
+
+			assert.strictEqual((await repository.getConfigs()).filter(config => config.key === key).length, 2);
+		});
+	});
+
+	describe('associateBaseBranchWithBranch', function () {
+		it('replaces base branch metadata instead of appending values', async function () {
+			await PullRequestGitHelper.associateBaseBranchWithBranch(repository, 'feature', { owner: 'owner', repo: 'name', branch: 'main' });
+			await PullRequestGitHelper.associateBaseBranchWithBranch(repository, 'feature', { owner: 'owner', repo: 'name', branch: 'main' });
+			await PullRequestGitHelper.associateBaseBranchWithBranch(repository, 'feature', { owner: 'owner', repo: 'name', branch: 'next' });
+
+			const key = 'branch.feature.github-pr-base-branch';
+			assert.deepStrictEqual((await repository.getConfigs()).filter(config => config.key === key), [
+				{ key, value: 'owner#name#next' },
+			]);
+		});
+	});
+
 	describe('getMatchingPullRequestMetadataForBranch', function () {
 		it('returns the highest-numbered PR when duplicate config entries exist for the branch', async function () {
 			// Simulate the case where a branch name has been associated with multiple