diff --git a/package.json b/package.json
index d26b6bd79b0c..78fa43cc621e 100644
--- a/package.json
+++ b/package.json
@@ -1051,6 +1051,7 @@
     "cypress-react-selector": "^3.0.0",
     "cypress-real-events": "^1.7.6",
     "cypress-recurse": "^1.26.0",
+    "date-fns": "^2.29.3",
     "debug": "^2.6.9",
     "delete-empty": "^2.0.0",
     "dependency-check": "^4.1.0",
diff --git a/packages/kbn-babel-register/BUILD.bazel b/packages/kbn-babel-register/BUILD.bazel
index a151c4e54c61..f97499a481ba 100644
--- a/packages/kbn-babel-register/BUILD.bazel
+++ b/packages/kbn-babel-register/BUILD.bazel
@@ -35,6 +35,7 @@ BUNDLER_DEPS = [
   "@npm//chalk",
   "@npm//pirates",
   "@npm//lmdb",
+  "@npm//date-fns",
   "@npm//source-map-support",
   "//packages/kbn-repo-packages",
   "//packages/kbn-repo-info",
diff --git a/packages/kbn-babel-register/cache/index.js b/packages/kbn-babel-register/cache/index.js
index 7838a6c89028..ea03e1396361 100644
--- a/packages/kbn-babel-register/cache/index.js
+++ b/packages/kbn-babel-register/cache/index.js
@@ -10,7 +10,6 @@ const Fs = require('fs');
 const Path = require('path');
 const Crypto = require('crypto');
 
-const { readHashOfPackageMap } = require('@kbn/repo-packages');
 const babel = require('@babel/core');
 const peggy = require('@kbn/peggy');
 const { REPO_ROOT, UPSTREAM_BRANCH } = require('@kbn/repo-info');
@@ -25,7 +24,6 @@ const { getBabelOptions } = require('@kbn/babel-transform');
  */
 function determineCachePrefix() {
   const json = JSON.stringify({
-    synthPkgMapHash: readHashOfPackageMap(),
     babelVersion: babel.version,
     peggyVersion: peggy.version,
     // get a config for a fake js, ts, and tsx file to make sure we
@@ -63,8 +61,7 @@ function getCache() {
   if (lmdbAvailable()) {
     log?.write('lmdb is available, using lmdb cache\n');
     return new (require('./lmdb_cache').LmdbCache)({
-      pathRoot: REPO_ROOT,
-      dir: Path.resolve(REPO_ROOT, 'data/babel_register_cache_v1', UPSTREAM_BRANCH),
+      dir: Path.resolve(REPO_ROOT, 'data/babel_register_cache', UPSTREAM_BRANCH),
       prefix: determineCachePrefix(),
       log,
     });
diff --git a/packages/kbn-babel-register/cache/lmdb_cache.js b/packages/kbn-babel-register/cache/lmdb_cache.js
index 1c69ba1ed12a..fe2179a59137 100644
--- a/packages/kbn-babel-register/cache/lmdb_cache.js
+++ b/packages/kbn-babel-register/cache/lmdb_cache.js
@@ -7,17 +7,21 @@
  */
 
 const Path = require('path');
+const Crypto = require('crypto');
+const startOfDay = /** @type {import('date-fns/startOfDay').default} */ (
+  /** @type {unknown} */ (require('date-fns/startOfDay'))
+);
 
 const chalk = require('chalk');
 const LmdbStore = require('lmdb');
 
-const GLOBAL_ATIME = `${Date.now()}`;
+const GLOBAL_ATIME = startOfDay(new Date()).valueOf();
 const MINUTE = 1000 * 60;
 const HOUR = MINUTE * 60;
 const DAY = HOUR * 24;
 
 /** @typedef {import('./types').Cache} CacheInterface */
-/** @typedef {import('lmdb').Database<string, string>} Db */
+/** @typedef {import('lmdb').Database<import('./types').CacheEntry, string>} Db */
 
 /**
  * @param {Db} db
@@ -31,63 +35,29 @@ const dbName = (db) =>
  * @implements {CacheInterface}
  */
 class LmdbCache {
-  /** @type {import('lmdb').RootDatabase<string, string>} */
-  #codes;
-  /** @type {Db} */
-  #atimes;
-  /** @type {Db} */
-  #mtimes;
-  /** @type {Db} */
-  #sourceMaps;
-  /** @type {string} */
-  #pathRoot;
-  /** @type {string} */
-  #prefix;
+  /** @type {import('lmdb').RootDatabase<import('./types').CacheEntry, string>} */
+  #db;
   /** @type {import('stream').Writable | undefined} */
   #log;
-  /** @type {ReturnType<typeof setTimeout>} */
-  #timer;
+  /** @type {string} */
+  #prefix;
 
   /**
    * @param {import('./types').CacheConfig} config
    */
   constructor(config) {
-    if (!Path.isAbsolute(config.pathRoot)) {
-      throw new Error('cache requires an absolute path to resolve paths relative to');
-    }
-
-    this.#pathRoot = config.pathRoot;
-    this.#prefix = config.prefix;
     this.#log = config.log;
-
-    this.#codes = LmdbStore.open(config.dir, {
-      name: 'codes',
-      encoding: 'string',
-      maxReaders: 500,
+    this.#prefix = config.prefix;
+    this.#db = LmdbStore.open(Path.resolve(config.dir, 'v5'), {
+      name: 'db',
+      encoding: 'json',
     });
 
-    // TODO: redundant 'name' syntax is necessary because of a bug that I have yet to fix
-    this.#atimes = this.#codes.openDB('atimes', {
-      name: 'atimes',
-      encoding: 'string',
-    });
-
-    this.#mtimes = this.#codes.openDB('mtimes', {
-      name: 'mtimes',
-      encoding: 'string',
-    });
-
-    this.#sourceMaps = this.#codes.openDB('sourceMaps', {
-      name: 'sourceMaps',
-      encoding: 'string',
-    });
-
-    // after the process has been running for 30 minutes prune the
-    // keys which haven't been used in 30 days. We use `unref()` to
-    // make sure this timer doesn't hold other processes open
-    // unexpectedly
-    this.#timer = setTimeout(() => {
-      this.#pruneOldKeys().catch((error) => {
+    const lastClean = this.#db.get('@last clean');
+    if (!lastClean || lastClean[0] < GLOBAL_ATIME - 7 * DAY) {
+      try {
+        this.#pruneOldKeys();
+      } catch (error) {
         process.stderr.write(`
 Failed to cleanup @kbn/babel-register cache:
 
@@ -95,83 +65,60 @@ Failed to cleanup @kbn/babel-register cache:
 
 To eliminate this problem you may want to delete the "${Path.relative(process.cwd(), config.dir)}"
 directory and report this error to the Operations team.\n`);
-      });
-    }, 30 * MINUTE);
-
-    // timer.unref is not defined in jest which emulates the dom by default
-    if (typeof this.#timer.unref === 'function') {
-      this.#timer.unref();
+      } finally {
+        this.#db.putSync('@last clean', [GLOBAL_ATIME, '', {}]);
+      }
     }
   }
 
   /**
+   * Get the cache key of the path and source from disk of a file
    * @param {string} path
+   * @param {string} source
+   * @returns {string}
    */
-  getMtime(path) {
-    return this.#safeGet(this.#mtimes, this.#getKey(path));
+  getKey(path, source) {
+    return `${this.#prefix}:${Crypto.createHash('sha1').update(path).update(source).digest('hex')}`;
   }
 
   /**
-   * @param {string} path
+   * @param {string} key
+   * @returns {string|undefined}
    */
-  getCode(path) {
-    const key = this.#getKey(path);
-    const code = this.#safeGet(this.#codes, key);
+  getCode(key) {
+    const entry = this.#safeGet(this.#db, key);
 
-    if (code !== undefined) {
+    if (entry !== undefined && entry[0] !== GLOBAL_ATIME) {
       // when we use a file from the cache set the "atime" of that cache entry
       // so that we know which cache items we use and which haven't been
-      // touched in a long time (currently 30 days)
-      this.#safePut(this.#atimes, key, GLOBAL_ATIME);
+      // used in a long time (currently 30 days)
+      this.#safePut(this.#db, key, [GLOBAL_ATIME, entry[1], entry[2]]);
     }
 
-    return code;
+    return entry?.[1];
   }
 
   /**
-   * @param {string} path
+   * @param {string} key
+   * @returns {object|undefined}
    */
-  getSourceMap(path) {
-    const map = this.#safeGet(this.#sourceMaps, this.#getKey(path));
-    if (typeof map === 'string') {
-      return JSON.parse(map);
-    }
-  }
-
-  close() {
-    clearTimeout(this.#timer);
-  }
-
-  /**
-   * @param {string} path
-   * @param {{ mtime: string; code: string; map?: any }} file
-   */
-  async update(path, file) {
-    const key = this.#getKey(path);
-
-    this.#safePut(this.#atimes, key, GLOBAL_ATIME);
-    this.#safePut(this.#mtimes, key, file.mtime);
-    this.#safePut(this.#codes, key, file.code);
-
-    if (file.map) {
-      this.#safePut(this.#sourceMaps, key, JSON.stringify(file.map));
+  getSourceMap(key) {
+    const entry = this.#safeGet(this.#db, key);
+    if (entry) {
+      return entry[2];
     }
   }
 
   /**
-   * @param {string} path
+   * @param {string} key
+   * @param {{ code: string, map: object }} entry
    */
-  #getKey(path) {
-    const normalizedPath =
-      Path.sep !== '/'
-        ? Path.relative(this.#pathRoot, path).split(Path.sep).join('/')
-        : Path.relative(this.#pathRoot, path);
-
-    return `${this.#prefix}:${normalizedPath}`;
+  async update(key, entry) {
+    this.#safePut(this.#db, key, [GLOBAL_ATIME, entry.code, entry.map]);
   }
 
   /**
-   * @param {LmdbStore.Database<string, string>} db
+   * @param {Db} db
    * @param {string} key
    */
   #safeGet(db, key) {
@@ -190,9 +137,9 @@ directory and report this error to the Operations team.\n`);
   }
 
   /**
-   * @param {LmdbStore.Database<string, string>} db
+   * @param {Db} db
    * @param {string} key
-   * @param {string} value
+   * @param {import('./types').CacheEntry} value
    */
   #safePut(db, key, value) {
     try {
@@ -205,7 +152,7 @@ directory and report this error to the Operations team.\n`);
 
   /**
    * @param {string} type
-   * @param {LmdbStore.Database<string, string>} db
+   * @param {Db} db
    * @param {string} key
    */
   #debug(type, db, key) {
@@ -214,7 +161,7 @@ directory and report this error to the Operations team.\n`);
 
   /**
    * @param {'GET' | 'PUT'} type
-   * @param {LmdbStore.Database<string, string>} db
+   * @param {Db} db
    * @param {string} key
    * @param {Error} error
    */
@@ -227,51 +174,36 @@ directory and report this error to the Operations team.\n`);
     );
   }
 
-  async #pruneOldKeys() {
-    try {
-      const ATIME_LIMIT = Date.now() - 30 * DAY;
-      const BATCH_SIZE = 1000;
+  #pruneOldKeys() {
+    const ATIME_LIMIT = Date.now() - 30 * DAY;
 
-      /** @type {string[]} */
-      const validKeys = [];
-      /** @type {string[]} */
-      const invalidKeys = [];
+    /** @type {string[]} */
+    const toDelete = [];
+    const flushDeletes = () => {
+      if (!toDelete.length) {
+        return;
+      }
 
-      for (const { key, value } of this.#atimes.getRange()) {
-        const atime = parseInt(`${value}`, 10);
-        if (Number.isNaN(atime) || atime < ATIME_LIMIT) {
-          invalidKeys.push(key);
-        } else {
-          validKeys.push(key);
+      this.#db.transactionSync(() => {
+        for (const key of toDelete) {
+          this.#db.removeSync(key);
         }
+      });
+    };
 
-        if (validKeys.length + invalidKeys.length >= BATCH_SIZE) {
-          const promises = new Set();
+    for (const { key, value } of this.#db.getRange()) {
+      if (Number.isNaN(value[0]) || value[0] < ATIME_LIMIT) {
+        toDelete.push(key);
 
-          if (invalidKeys.length) {
-            for (const k of invalidKeys) {
-              // all these promises are the same currently, so Set() will
-              // optimise this to a single promise, but I wouldn't be shocked
-              // if a future version starts returning independent promises so
-              // this is just for some future-proofing
-              promises.add(this.#atimes.remove(k));
-              promises.add(this.#mtimes.remove(k));
-              promises.add(this.#codes.remove(k));
-              promises.add(this.#sourceMaps.remove(k));
-            }
-          } else {
-            // delay a smidge to allow other things to happen before the next batch of checks
-            promises.add(new Promise((resolve) => setTimeout(resolve, 1)));
-          }
-
-          invalidKeys.length = 0;
-          validKeys.length = 0;
-          await Promise.all(Array.from(promises));
+        // flush deletes early if there are many deleted
+        if (toDelete.length > 10_000) {
+          flushDeletes();
         }
       }
-    } catch {
-      // ignore errors, the cache is totally disposable and will rebuild if there is some sort of corruption
     }
+
+    // delete all the old keys
+    flushDeletes();
   }
 }
 
diff --git a/packages/kbn-babel-register/cache/lmdb_cache.test.ts b/packages/kbn-babel-register/cache/lmdb_cache.test.ts
index d752e45879ae..e1a8401ea946 100644
--- a/packages/kbn-babel-register/cache/lmdb_cache.test.ts
+++ b/packages/kbn-babel-register/cache/lmdb_cache.test.ts
@@ -18,7 +18,7 @@ const DIR = Path.resolve(__dirname, '../__tmp__/cache');
 const makeTestLog = () => {
   const log = Object.assign(
     new Writable({
-      write(chunk, enc, cb) {
+      write(chunk, _, cb) {
         log.output += chunk;
         cb();
       },
@@ -39,50 +39,35 @@ const makeCache = (...options: ConstructorParameters<typeof LmdbCache>) => {
 };
 
 beforeEach(async () => await del(DIR));
-afterEach(async () => {
-  await del(DIR);
-  for (const instance of instances) {
-    instance.close();
-  }
-  instances.length = 0;
-});
+afterEach(async () => await del(DIR));
 
 it('returns undefined until values are set', async () => {
   const path = '/foo/bar.js';
-  const mtime = new Date().toJSON();
+  const source = `console.log("hi, hello")`;
   const log = makeTestLog();
   const cache = makeCache({
     dir: DIR,
     prefix: 'prefix',
     log,
-    pathRoot: '/foo/',
   });
 
-  expect(cache.getMtime(path)).toBe(undefined);
-  expect(cache.getCode(path)).toBe(undefined);
-  expect(cache.getSourceMap(path)).toBe(undefined);
+  const key = cache.getKey(path, source);
+  expect(cache.getCode(key)).toBe(undefined);
+  expect(cache.getSourceMap(key)).toBe(undefined);
 
-  await cache.update(path, {
-    mtime,
+  await cache.update(key, {
     code: 'var x = 1',
     map: { foo: 'bar' },
   });
 
-  expect(cache.getMtime(path)).toBe(mtime);
-  expect(cache.getCode(path)).toBe('var x = 1');
-  expect(cache.getSourceMap(path)).toEqual({ foo: 'bar' });
+  expect(cache.getCode(key)).toBe('var x = 1');
+  expect(cache.getSourceMap(key)).toEqual({ foo: 'bar' });
   expect(log.output).toMatchInlineSnapshot(`
-    "MISS   [mtimes]   prefix:bar.js
-    MISS   [codes]   prefix:bar.js
-    MISS   [sourceMaps]   prefix:bar.js
-    PUT   [atimes]   prefix:bar.js
-    PUT   [mtimes]   prefix:bar.js
-    PUT   [codes]   prefix:bar.js
-    PUT   [sourceMaps]   prefix:bar.js
-    HIT   [mtimes]   prefix:bar.js
-    HIT   [codes]   prefix:bar.js
-    PUT   [atimes]   prefix:bar.js
-    HIT   [sourceMaps]   prefix:bar.js
+    "MISS   [db]   prefix:05a4b8198c4ec215d54d94681ef00ca9ecb45931
+    MISS   [db]   prefix:05a4b8198c4ec215d54d94681ef00ca9ecb45931
+    PUT   [db]   prefix:05a4b8198c4ec215d54d94681ef00ca9ecb45931
+    HIT   [db]   prefix:05a4b8198c4ec215d54d94681ef00ca9ecb45931
+    HIT   [db]   prefix:05a4b8198c4ec215d54d94681ef00ca9ecb45931
     "
   `);
 });
diff --git a/packages/kbn-babel-register/cache/no_cache_cache.js b/packages/kbn-babel-register/cache/no_cache_cache.js
index b4608e866d3b..5d5aac93af0f 100644
--- a/packages/kbn-babel-register/cache/no_cache_cache.js
+++ b/packages/kbn-babel-register/cache/no_cache_cache.js
@@ -12,6 +12,10 @@
  * @implements {CacheInterface}
  */
 class NoCacheCache {
+  getKey() {
+    return '';
+  }
+
   getCode() {
     return undefined;
   }
diff --git a/packages/kbn-babel-register/cache/types.ts b/packages/kbn-babel-register/cache/types.ts
index 6438662ae2d6..5189d3e7f391 100644
--- a/packages/kbn-babel-register/cache/types.ts
+++ b/packages/kbn-babel-register/cache/types.ts
@@ -9,16 +9,16 @@
 import { Writable } from 'stream';
 
 export interface CacheConfig {
-  pathRoot: string;
   dir: string;
   prefix: string;
   log?: Writable;
 }
 
 export interface Cache {
-  getMtime(path: string): string | undefined;
-  getCode(path: string): string | undefined;
-  getSourceMap(path: string): object | undefined;
-  update(path: string, opts: { mtime: string; code: string; map?: any }): Promise<void>;
-  close(): void;
+  getKey(path: string, source: string): string;
+  getCode(key: string): string | undefined;
+  getSourceMap(key: string): object | undefined;
+  update(key: string, entry: { code: string; map?: object | null }): Promise<void>;
 }
+
+export type CacheEntry = [atime: number, code: string, sourceMap: object];
diff --git a/packages/kbn-babel-register/index.js b/packages/kbn-babel-register/index.js
index ba20e1f1b18f..457b0895919a 100644
--- a/packages/kbn-babel-register/index.js
+++ b/packages/kbn-babel-register/index.js
@@ -41,6 +41,7 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
+const Fs = require('fs');
 const Path = require('path');
 
 const { addHook } = require('pirates');
@@ -105,7 +106,18 @@ function install(options = undefined) {
     environment: 'node',
     // @ts-expect-error bad source-map-support types
     retrieveSourceMap(path) {
-      const map = cache.getSourceMap(path);
+      if (!Path.isAbsolute(path)) {
+        return null;
+      }
+
+      let source;
+      try {
+        source = Fs.readFileSync(path, 'utf8');
+      } catch {
+        return null;
+      }
+
+      const map = cache.getSourceMap(cache.getKey(path, source));
       return map ? { map, url: null } : null;
     },
   });
diff --git a/packages/kbn-babel-register/transforms/babel.js b/packages/kbn-babel-register/transforms/babel.js
index a1557bd52889..8328a60d477b 100644
--- a/packages/kbn-babel-register/transforms/babel.js
+++ b/packages/kbn-babel-register/transforms/babel.js
@@ -6,25 +6,18 @@
  * Side Public License, v 1.
  */
 
-const Fs = require('fs');
-
 const { transformCode } = require('@kbn/babel-transform');
 
 /** @type {import('./types').Transform} */
 const babelTransform = (path, source, cache) => {
-  const mtime = `${Fs.statSync(path).mtimeMs}`;
-
-  if (cache.getMtime(path) === mtime) {
-    const code = cache.getCode(path);
-    if (code) {
-      return code;
-    }
+  const key = cache.getKey(path, source);
+  const cached = cache.getCode(key);
+  if (cached) {
+    return cached;
   }
 
   const result = transformCode(path, source);
-
-  cache.update(path, {
-    mtime,
+  cache.update(key, {
     code: result.code,
     map: result.map,
   });
diff --git a/packages/kbn-babel-register/transforms/peggy.js b/packages/kbn-babel-register/transforms/peggy.js
index b87676ca03bc..6df30526d36f 100644
--- a/packages/kbn-babel-register/transforms/peggy.js
+++ b/packages/kbn-babel-register/transforms/peggy.js
@@ -6,27 +6,16 @@
  * Side Public License, v 1.
  */
 
-const Fs = require('fs');
-const Crypto = require('crypto');
-
 const Peggy = require('@kbn/peggy');
 
 /** @type {import('./types').Transform} */
 const peggyTransform = (path, source, cache) => {
   const config = Peggy.findConfigFile(path);
-  const mtime = `${Fs.statSync(path).mtimeMs}`;
-  const key = !config
-    ? path
-    : `${path}.config.${Crypto.createHash('sha256')
-        .update(config.source)
-        .digest('hex')
-        .slice(0, 8)}`;
+  const key = cache.getKey(path, source);
 
-  if (cache.getMtime(key) === mtime) {
-    const code = cache.getCode(key);
-    if (code) {
-      return code;
-    }
+  const cached = cache.getCode(key);
+  if (cached) {
+    return cached;
   }
 
   const code = Peggy.getJsSourceSync({
@@ -40,7 +29,6 @@ const peggyTransform = (path, source, cache) => {
 
   cache.update(key, {
     code,
-    mtime,
   });
 
   return code;
diff --git a/packages/kbn-babel-register/tsconfig.json b/packages/kbn-babel-register/tsconfig.json
index 09576d2904a8..96e50650eee6 100644
--- a/packages/kbn-babel-register/tsconfig.json
+++ b/packages/kbn-babel-register/tsconfig.json
@@ -16,7 +16,6 @@
     "@kbn/repo-info",
     "@kbn/babel-transform",
     "@kbn/peggy",
-    "@kbn/repo-packages",
   ],
   "exclude": [
     "target/**/*",
diff --git a/packages/kbn-cli-dev-mode/src/watcher.ts b/packages/kbn-cli-dev-mode/src/watcher.ts
index 660022b6fc57..e4ade054b473 100644
--- a/packages/kbn-cli-dev-mode/src/watcher.ts
+++ b/packages/kbn-cli-dev-mode/src/watcher.ts
@@ -77,7 +77,7 @@ export class Watcher {
 
           // ignore changes in any devOnly package, these can't power the server so we can ignore them
           if (pkg?.devOnly) {
-            return;
+            return pkg.id === '@kbn/babel-register';
           }
 
           const result = this.classifier.classify(event.path);
diff --git a/yarn.lock b/yarn.lock
index fa46dea2940e..8b1d994f4f69 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -12314,6 +12314,11 @@ date-fns@^1.27.2, date-fns@^1.30.1:
   resolved "https://registry.yarnpkg.com/date-fns/-/date-fns-1.30.1.tgz#2e71bf0b119153dbb4cc4e88d9ea5acfb50dc05c"
   integrity sha512-hBSVCvSmWC+QypYObzwGOd9wqdDpOt+0wl0KbU+R+uuZBS1jN8VsD1ss3irQDknRj5NvxiTF6oj/nDRnN/UQNw==
 
+date-fns@^2.29.3:
+  version "2.29.3"
+  resolved "https://registry.yarnpkg.com/date-fns/-/date-fns-2.29.3.tgz#27402d2fc67eb442b511b70bbdf98e6411cd68a8"
+  integrity sha512-dDCnyH2WnnKusqvZZ6+jA1O51Ibt8ZMRNkDZdyAyK4YfbDwa/cEmuztzG5pk6hqlp9aSBPYcjOlktquahGwGeA==
+
 date-now@^0.1.4:
   version "0.1.4"
   resolved "https://registry.yarnpkg.com/date-now/-/date-now-0.1.4.tgz#eaf439fd4d4848ad74e5cc7dbef200672b9e345b"