diff --git a/mcp/checkout.ts b/mcp/checkout.ts
index ae47dc6..4ce2c26 100644
--- a/mcp/checkout.ts
+++ b/mcp/checkout.ts
@@ -5,7 +5,7 @@ import type { Octokit, RestEndpointMethodTypes } from "@octokit/rest";
 import { type } from "arktype";
 import { log } from "../utils/cli.ts";
 import { countLines, createDiffCoverageState } from "../utils/diffCoverage.ts";
-import { $git } from "../utils/gitAuth.ts";
+import { $git, $gitFetchWithDeepen } from "../utils/gitAuth.ts";
 import { executeLifecycleHook } from "../utils/lifecycle.ts";
 import { computeIncrementalDiff } from "../utils/rangeDiff.ts";
 import { retry } from "../utils/retry.ts";
@@ -259,10 +259,10 @@ async function ensureBeforeShaReachable(params: EnsureBeforeShaParams): Promise<
       sha: params.sha,
       ref: tempBranch,
     });
-    await $git(
-      "fetch",
+    await $gitFetchWithDeepen(
       ["--no-tags", ...(params.isShallow ? ["--depth=1"] : []), "origin", tempBranch],
-      { token: params.gitToken }
+      { token: params.gitToken },
+      `before_sha temp branch ${tempBranch}`
     );
     log.debug(`» fetched before_sha via temp branch ${tempBranch}`);
     return true;
@@ -410,9 +410,17 @@ export async function checkoutPrBranch(
   toolState.checkoutSha = $("git", ["rev-parse", "HEAD"], { log: false }).trim();
   const alreadyOnBranch = toolState.checkoutSha === pr.headSha;
 
-  // fetch base branch so origin/<base> exists for diff operations
+  // fetch base branch so origin/<base> exists for diff operations.
+  // wrap with deepen-retry: on shallow clones (the actions/checkout default
+  // is depth=1), repos with deep PR ancestry can't reach the baseRef tip in
+  // a single round trip, surfacing as `Could not read <sha>` / `remote did
+  // not send all necessary objects` (issue #656).
   log.debug(`» fetching base branch (${pr.baseRef})...`);
-  await $git("fetch", ["--no-tags", "origin", pr.baseRef], { token: gitToken });
+  await $gitFetchWithDeepen(
+    ["--no-tags", "origin", pr.baseRef],
+    { token: gitToken },
+    `base branch ${pr.baseRef}`
+  );
 
   // alreadyOnBranch only matches for repeated checkout_pr calls for the same PR in one session
   // (without the tip moving), or if an external setup already checked out the PR head.
@@ -426,14 +434,21 @@ export async function checkoutPrBranch(
     // -B creates or resets the branch to match origin/baseBranch
     $("git", ["checkout", "-B", pr.baseRef, `origin/${pr.baseRef}`], { log: false });
 
-    // fetch PR branch using pull/{n}/head refspec (works for both fork and same-repo PRs)
+    // fetch PR branch using pull/{n}/head refspec (works for both fork and same-repo PRs).
+    // two transient classes wrap this fetch:
+    //   - shallow-unreachable (`Could not read <sha>` etc.) — handled by the
+    //     inner `$gitFetchWithDeepen` deepen-retry (one shot, see issue #656)
+    //   - pull/N/head webhook race (`couldn't find remote ref pull/N/head`) —
+    //     handled by the outer retry below (see issue #591)
     log.debug(`» fetching PR #${pr.number} (${localBranch})...`);
     await retry(
       async () => {
         try {
-          await $git("fetch", ["--no-tags", "origin", `+pull/${pr.number}/head:${localBranch}`], {
-            token: gitToken,
-          });
+          await $gitFetchWithDeepen(
+            ["--no-tags", "origin", `+pull/${pr.number}/head:${localBranch}`],
+            { token: gitToken },
+            `PR #${pr.number}`
+          );
         } catch (e) {
           // on the webhook race, check whether the PR still matches what we
           // dispatched on. if it's been closed/merged or the head SHA moved,
diff --git a/mcp/git.ts b/mcp/git.ts
index da5cdd4..5e96ba5 100644
--- a/mcp/git.ts
+++ b/mcp/git.ts
@@ -2,7 +2,7 @@ import { regex } from "arkregex";
 import { type } from "arktype";
 import type { StoredPushDest } from "../toolState.ts";
 import { log } from "../utils/cli.ts";
-import { $git } from "../utils/gitAuth.ts";
+import { $git, $gitFetchWithDeepen } from "../utils/gitAuth.ts";
 import { executeLifecycleHook } from "../utils/lifecycle.ts";
 import { $ } from "../utils/shell.ts";
 import type { ToolContext } from "./server.ts";
@@ -510,21 +510,6 @@ const GitFetch = type({
   depth: type.number.describe("Fetch depth (for shallow clones)").optional(),
 });
 
-// when an agent-supplied depth is too shallow to reach the merge base, git
-// surfaces "Could not read <sha>" and "remote did not send all necessary
-// objects". detect both wordings so a single deepen retry can recover before
-// the error reaches the agent (issue #564). git emits the full OID via
-// oid_to_hex, so the bound is 40 (SHA-1) or 64 (SHA-256).
-const SHALLOW_UNREACHABLE_PATTERNS: RegExp[] = [
-  /Could not read [a-f0-9]{40,64}/,
-  /remote did not send all necessary objects/,
-];
-
-// large enough to clear the merge base on most real-world PRs without
-// downloading the full history; matches the fallback used by checkoutPrBranch
-// when the compare API is unavailable.
-const DEEPEN_RETRY_DEPTH = 1000;
-
 export function GitFetchTool(ctx: ToolContext) {
   return tool({
     name: "git_fetch",
@@ -538,22 +523,7 @@ export function GitFetchTool(ctx: ToolContext) {
       if (params.depth !== undefined) {
         fetchArgs.push(`--depth=${params.depth}`);
       }
-      try {
-        await $git("fetch", fetchArgs, { token: ctx.gitToken });
-      } catch (err) {
-        const msg = err instanceof Error ? err.message : String(err);
-        const isShallowUnreachable = SHALLOW_UNREACHABLE_PATTERNS.some((p) => p.test(msg));
-        const isShallow =
-          isShallowUnreachable &&
-          $("git", ["rev-parse", "--is-shallow-repository"], { log: false }).trim() === "true";
-        if (!isShallow) throw err;
-        log.info(
-          `» git_fetch hit shallow-unreachable error, retrying with --deepen=${DEEPEN_RETRY_DEPTH}`
-        );
-        await $git("fetch", [`--deepen=${DEEPEN_RETRY_DEPTH}`, "--no-tags", "origin", params.ref], {
-          token: ctx.gitToken,
-        });
-      }
+      await $gitFetchWithDeepen(fetchArgs, { token: ctx.gitToken }, "git_fetch");
       return { success: true, ref: params.ref };
     }),
   });
diff --git a/utils/gitAuth.ts b/utils/gitAuth.ts
index 8d79bac..20b27ad 100644
--- a/utils/gitAuth.ts
+++ b/utils/gitAuth.ts
@@ -14,6 +14,7 @@ import { readFileSync, realpathSync, unlinkSync } from "node:fs";
 import { log } from "./cli.ts";
 import type { GitAuthServer } from "./gitAuthServer.ts";
 import { filterEnv } from "./secrets.ts";
+import { $ } from "./shell.ts";
 import { spawn } from "./subprocess.ts";
 
 type SafeGitSubcommand = "fetch" | "push";
@@ -181,3 +182,56 @@ export async function $git(
     }
   }
 }
+
+/**
+ * shallow-clone unreachable: when an existing local depth is too shallow for
+ * git to traverse to the requested ref's ancestry, the remote walk fails with
+ * one of these wordings (git emits the full OID via oid_to_hex, so the bound
+ * is 40 for SHA-1 or 64 for SHA-256). detecting both lets a single deepen
+ * retry recover before the error reaches the agent — see issue #564 for the
+ * original `git_fetch` precedent and #656 for the `checkout_pr` follow-up.
+ */
+export const SHALLOW_UNREACHABLE_PATTERNS: RegExp[] = [
+  /Could not read [a-f0-9]{40,64}/,
+  /remote did not send all necessary objects/,
+];
+
+/**
+ * large enough to clear the merge base on most real-world PRs without
+ * downloading the full history; matches the fallback used by
+ * `checkoutPrBranch` when the GitHub compare API is unavailable.
+ */
+export const DEEPEN_RETRY_DEPTH = 1000;
+
+/**
+ * authenticated `git fetch` that recovers from shallow-unreachable errors
+ * by retrying once with `--deepen=1000`. callers pass the same args they
+ * would to `$git("fetch", ...)`; on shallow-unreachable failures in a
+ * shallow repo, the second attempt prepends `--deepen=N` and strips any
+ * caller-supplied `--depth=` (the two flags are mutually exclusive, and
+ * the caller's depth is what got us into this mess).
+ *
+ * non-shallow-unreachable errors and non-shallow repos rethrow unchanged,
+ * so this is safe to wrap any fetch without changing fast-path behavior.
+ */
+export async function $gitFetchWithDeepen(
+  args: string[],
+  options: GitAuthOptions,
+  label?: string
+): Promise<GitResult> {
+  try {
+    return await $git("fetch", args, options);
+  } catch (err) {
+    const msg = err instanceof Error ? err.message : String(err);
+    const isShallowUnreachable = SHALLOW_UNREACHABLE_PATTERNS.some((p) => p.test(msg));
+    if (!isShallowUnreachable) throw err;
+    const isShallow =
+      $("git", ["rev-parse", "--is-shallow-repository"], { log: false }).trim() === "true";
+    if (!isShallow) throw err;
+    log.info(
+      `» ${label ?? "git fetch"} hit shallow-unreachable error, retrying with --deepen=${DEEPEN_RETRY_DEPTH}`
+    );
+    const retryArgs = args.filter((a) => !a.startsWith("--depth="));
+    return await $git("fetch", [`--deepen=${DEEPEN_RETRY_DEPTH}`, ...retryArgs], options);
+  }
+}