diff --git a/README.md b/README.md
index a7acfb4..e7ea184 100644
--- a/README.md
+++ b/README.md
@@ -106,6 +106,14 @@ string, that should return a
 is used to store the index state of each hypercore. (Index state is stored as a
 bitfield).
 
+#### opts.reindex
+
+_Optional_\
+Type: `boolean`
+
+If `true`, the cores, and any new ones that are added, will be reindexed from
+scratch.
+
 #### opts.maxBatch
 
 _Optional_\
diff --git a/index.js b/index.js
index 3eb0ed3..2ad59ff 100644
--- a/index.js
+++ b/index.js
@@ -34,6 +34,7 @@ class MultiCoreIndexer extends TypedEmitter {
   #rateMeasurementStart = Date.now()
   #rate = 0
   #createStorage
+  #reindex
   /** @type {IndexState | undefined} */
   #prevEmittedState
   #emitStateBound
@@ -46,13 +47,18 @@ class MultiCoreIndexer extends TypedEmitter {
    * @param {object} opts
    * @param {(entries: Entry<T>[]) => Promise<void>} opts.batch
    * @param {StorageParam} opts.storage
+   * @param {boolean} [opts.reindex]
    * @param {number} [opts.maxBatch=100]
    */
-  constructor(cores, { batch, maxBatch = DEFAULT_BATCH_SIZE, storage }) {
+  constructor(
+    cores,
+    { batch, maxBatch = DEFAULT_BATCH_SIZE, storage, reindex = false }
+  ) {
     super()
     this.#createStorage = MultiCoreIndexer.defaultStorage(storage)
+    this.#reindex = reindex
     const coreIndexStreams = cores.map((core) => {
-      return new CoreIndexStream(core, this.#createStorage)
+      return new CoreIndexStream(core, this.#createStorage, reindex)
     })
     this.#indexStream = new MultiCoreIndexStream(coreIndexStreams, {
       highWaterMark: maxBatch,
@@ -95,7 +101,11 @@ class MultiCoreIndexer extends TypedEmitter {
    */
   addCore(core) {
     this.#assertOpen('Cannot add core after closing')
-    const coreIndexStream = new CoreIndexStream(core, this.#createStorage)
+    const coreIndexStream = new CoreIndexStream(
+      core,
+      this.#createStorage,
+      this.#reindex
+    )
     this.#indexStream.addStream(coreIndexStream)
   }
 
diff --git a/lib/core-index-stream.js b/lib/core-index-stream.js
index 1e09322..6b2884c 100644
--- a/lib/core-index-stream.js
+++ b/lib/core-index-stream.js
@@ -45,8 +45,9 @@ class CoreIndexStream extends Readable {
   /**
    * @param {import('hypercore')<T, any>} core
    * @param {(name: string) => import('random-access-storage')} createStorage
+   * @param {boolean} reindex
    */
-  constructor(core, createStorage) {
+  constructor(core, createStorage, reindex) {
     super({
       // Treat as object stream, count each object as size `1` so that the
       // `remaining` property can use the stream buffer to calculate how many
@@ -59,10 +60,15 @@ class CoreIndexStream extends Readable {
     this.#handleDownloadBound = this.#handleDownload.bind(this)
     this.#createStorage = async () => {
       await this.#core.ready()
+
       const { discoveryKey } = this.#core
       /* c8 ignore next: just to keep TS happy - after core.ready() this is set */
       if (!discoveryKey) throw new Error('Missing discovery key')
-      return createStorage(getStorageName(discoveryKey))
+      const storageName = getStorageName(discoveryKey)
+
+      if (reindex) await unlinkStorage(createStorage(storageName))
+
+      return createStorage(storageName)
     }
   }
 
diff --git a/test/multi-core-indexer.test.js b/test/multi-core-indexer.test.js
index fad72f5..a7a5b48 100644
--- a/test/multi-core-indexer.test.js
+++ b/test/multi-core-indexer.test.js
@@ -399,6 +399,48 @@ test('Entries are re-indexed if index storage unlinked', async () => {
   await indexer2.close()
 })
 
+test('Entries can be explicitly reindexed with a startup option', async (t) => {
+  const cores = await createMultiple(3)
+  const [core1, core2, core3] = cores
+  const expectedIn1And2 = new Set(await generateFixtures([core1, core2], 3))
+  const expectedIn3 = new Set(await generateFixtures([core3], 3))
+  const allExpected = new Set([...expectedIn1And2, ...expectedIn3])
+
+  const storage = ram.reusable()
+
+  /** @type {Set<Entry>} */ const entriesBeforeReindex = new Set()
+  const indexer1 = new MultiCoreIndexer(cores, {
+    batch: async (entries) => {
+      for (const entry of entries) entriesBeforeReindex.add(entry)
+    },
+    storage,
+  })
+  await indexer1.idle()
+  await indexer1.close()
+  assert.deepEqual(
+    entriesBeforeReindex,
+    allExpected,
+    'test setup: entries are indexed once'
+  )
+
+  /** @type {Set<Entry>} */ const entriesAfterReindex = new Set()
+  const indexer2 = new MultiCoreIndexer([core1, core2], {
+    batch: async (entries) => {
+      for (const entry of entries) entriesAfterReindex.add(entry)
+    },
+    storage,
+    reindex: true,
+  })
+  t.after(() => indexer2.close())
+
+  await indexer2.idle()
+  assert.deepEqual(entriesAfterReindex, expectedIn1And2)
+
+  indexer2.addCore(core3)
+  await indexer2.idle()
+  assert.deepEqual(entriesAfterReindex, allExpected)
+})
+
 test('Entries are batched to batchMax when indexing is slower than Hypercore reads', async () => {
   const cores = await createMultiple(5)
   await generateFixtures(cores, 500)
diff --git a/test/unit-tests/core-index-stream.test.js b/test/unit-tests/core-index-stream.test.js
index 58b2efa..2c24f34 100644
--- a/test/unit-tests/core-index-stream.test.js
+++ b/test/unit-tests/core-index-stream.test.js
@@ -14,7 +14,7 @@ const Hypercore = require('hypercore')
 
 test('stream.core', async () => {
   const a = await create()
-  const stream = new CoreIndexStream(a, () => new ram())
+  const stream = new CoreIndexStream(a, () => new ram(), false)
   assert.deepEqual(stream.core, a)
 })
 
@@ -25,7 +25,7 @@ test('destroy before open', async () => {
     return new ram()
   }
   const a = new Hypercore(() => new ram())
-  const stream = new CoreIndexStream(a, createStorage)
+  const stream = new CoreIndexStream(a, createStorage, false)
   stream.destroy()
   await once(stream, 'close')
   assert.equal(storageCreated, false, 'storage never created')
@@ -38,7 +38,7 @@ test('unlink before open', async () => {
     return new ram()
   }
   const core = new Hypercore(() => new ram())
-  const stream = new CoreIndexStream(core, createStorage)
+  const stream = new CoreIndexStream(core, createStorage, false)
   await stream.unlink()
   assert.equal(storageCreated, true, 'storage was created')
 })
@@ -50,15 +50,41 @@ test('Indexes all items already in a core', async () => {
   await a.append(blocks)
   /** @type {any[]} */
   const entries = []
-  const stream = new CoreIndexStream(a, () => new ram())
+  const stream = new CoreIndexStream(a, () => new ram(), false)
   stream.on('data', (entry) => entries.push(entry))
   await once(stream, 'drained')
   assert.deepEqual(entries, expected)
 })
 
+test('Re-indexing all items in a core', async () => {
+  const core = await create()
+  const blocks = generateFixture(0, 10)
+  const expected = blocksToExpected(blocks, core.key)
+  await core.append(blocks)
+
+  const storage = ram.reusable()
+
+  const stream1 = new CoreIndexStream(core, storage, false)
+  stream1.on('data', (entry) => {
+    stream1.setIndexed(entry.index)
+  })
+  await once(stream1, 'drained')
+  await stream1.destroy()
+
+  /** @type {any[]} */
+  const entries = []
+  const stream2 = new CoreIndexStream(core, storage, true)
+  stream2.on('data', (entry) => {
+    entries.push(entry)
+  })
+  await once(stream2, 'drained')
+
+  assert.deepEqual(entries, expected)
+})
+
 test("Empty core emits 'drained' event", async () => {
   const a = await create()
-  const stream = new CoreIndexStream(a, () => new ram())
+  const stream = new CoreIndexStream(a, () => new ram(), false)
   stream.resume()
   stream.on('indexing', assert.fail)
   await once(stream, 'drained')
@@ -72,7 +98,7 @@ test('.remaining property is accurate', async () => {
   await a.append(blocks)
   /** @type {any[]} */
   const entries = []
-  const stream = new CoreIndexStream(a, () => new ram())
+  const stream = new CoreIndexStream(a, () => new ram(), false)
   assert.equal(stream.remaining, totalBlocks)
   stream.on('data', (entry) => {
     entries.push(entry)
@@ -89,7 +115,7 @@ test('Indexes items appended after initial index', async () => {
   const blocks = generateFixture(0, 10)
   /** @type {any[]} */
   const entries = []
-  const stream = new CoreIndexStream(a, () => new ram())
+  const stream = new CoreIndexStream(a, () => new ram(), false)
   stream.on('data', (entry) => entries.push(entry))
   await once(stream, 'drained')
   assert.deepEqual(entries, [], 'no entries before append')
@@ -110,7 +136,7 @@ test('Readable stream from sparse hypercore', async () => {
   const range = b.download({ start: 5, end: 20 })
   await range.downloaded()
 
-  const stream = new CoreIndexStream(b, () => new ram())
+  const stream = new CoreIndexStream(b, () => new ram(), false)
   /** @type {Buffer[]} */
   const entries = []
   stream.on('data', (entry) => entries.push(entry.block))
@@ -134,7 +160,7 @@ test("'indexing' and 'drained' events are paired", async () => {
 
   replicate(a, b)
 
-  const stream = new CoreIndexStream(b, () => new ram())
+  const stream = new CoreIndexStream(b, () => new ram(), false)
   let indexingEvents = 0
   let idleEvents = 0
   stream.on('indexing', () => {
@@ -166,7 +192,7 @@ test('Appends from a replicated core are indexed', async () => {
   const range1 = b.download({ start: 0, end: b.length })
   await range1.downloaded()
 
-  const stream = new CoreIndexStream(b, () => new ram())
+  const stream = new CoreIndexStream(b, () => new ram(), false)
   /** @type {Buffer[]} */
   const entries = []
   stream.on('data', (entry) => entries.push(entry.block))
@@ -187,7 +213,7 @@ test('Maintains index state', async () => {
   /** @type {any[]} */
   const entries = []
   const storage = ram.reusable()
-  const stream1 = new CoreIndexStream(a, storage)
+  const stream1 = new CoreIndexStream(a, storage, false)
   stream1.on('data', (entry) => {
     entries.push(entry.block)
     stream1.setIndexed(entry.index)
@@ -200,7 +226,7 @@ test('Maintains index state', async () => {
   stream1.destroy()
   await once(stream1, 'close')
   await a.append(blocks.slice(500, 1000))
-  const stream2 = new CoreIndexStream(a, storage)
+  const stream2 = new CoreIndexStream(a, storage, false)
   stream2.on('data', (entry) => {
     entries.push(entry.block)
     stream2.setIndexed(entry.index)
diff --git a/test/unit-tests/multi-core-index-stream.test.js b/test/unit-tests/multi-core-index-stream.test.js
index a9c1859..9b1e187 100644
--- a/test/unit-tests/multi-core-index-stream.test.js
+++ b/test/unit-tests/multi-core-index-stream.test.js
@@ -19,7 +19,7 @@ test('Indexes all items already in a core', async () => {
   const cores = await createMultiple(5)
   const expected = await generateFixtures(cores, 1000)
   const indexStreams = cores.map(
-    (core) => new CoreIndexStream(core, () => new ram())
+    (core) => new CoreIndexStream(core, () => new ram(), false)
   )
   const entries = []
   const stream = new MultiCoreIndexStream(indexStreams)
@@ -44,7 +44,7 @@ test('Adding index streams after initialization', async () => {
   const cores = await createMultiple(3)
   const expected = await generateFixtures(cores, 100)
   const indexStreams = cores.map(
-    (core) => new CoreIndexStream(core, () => new ram())
+    (core) => new CoreIndexStream(core, () => new ram(), false)
   )
   const entries = []
   const stream = new MultiCoreIndexStream(indexStreams.slice(0, 2))
@@ -74,7 +74,7 @@ test('.remaining is as expected', async () => {
   const cores = await createMultiple(coreCount)
   const expected = await generateFixtures(cores, blockCount)
   const indexStreams = cores.map(
-    (core) => new CoreIndexStream(core, () => new ram())
+    (core) => new CoreIndexStream(core, () => new ram(), false)
   )
   const entries = []
   const stream = new MultiCoreIndexStream(indexStreams, { highWaterMark: 10 })
@@ -106,7 +106,7 @@ test('.remaining is as expected', async () => {
 test('Indexes items appended after initial index', async () => {
   const cores = await createMultiple(5)
   const indexStreams = cores.map(
-    (core) => new CoreIndexStream(core, () => new ram())
+    (core) => new CoreIndexStream(core, () => new ram(), false)
   )
   const entries = []
   const stream = new MultiCoreIndexStream(indexStreams, { highWaterMark: 10 })
@@ -138,7 +138,7 @@ test('index sparse hypercores', async () => {
   for (const core of remoteCores) {
     const range = core.download({ start: 5, end: 20 })
     await range.downloaded()
-    indexStreams.push(new CoreIndexStream(core, () => new ram()))
+    indexStreams.push(new CoreIndexStream(core, () => new ram(), false))
   }
   const entries = []
   const stream = new MultiCoreIndexStream(indexStreams, { highWaterMark: 10 })
@@ -172,7 +172,7 @@ test('Appends from a replicated core are indexed', async () => {
     await remote.update({ wait: true })
     const range = remote.download({ start: 0, end: remote.length })
     await range.downloaded()
-    indexStreams.push(new CoreIndexStream(core, () => new ram()))
+    indexStreams.push(new CoreIndexStream(core, () => new ram(), false))
   }
   const entries = []
   const stream = new MultiCoreIndexStream(indexStreams, { highWaterMark: 10 })
@@ -202,7 +202,7 @@ test('Maintains index state', async () => {
   for (const core of cores) {
     const storage = ram.reusable()
     storages.push(storage)
-    const indexStream = new CoreIndexStream(core, storage)
+    const indexStream = new CoreIndexStream(core, storage, false)
     indexStream.on('data', ({ index }) => {
       indexStream.setIndexed(index)
     })
@@ -211,7 +211,7 @@ test('Maintains index state', async () => {
   }
 
   const indexStreams = cores.map(
-    (core, i) => new CoreIndexStream(core, storages[i])
+    (core, i) => new CoreIndexStream(core, storages[i], false)
   )
   const stream = new MultiCoreIndexStream(indexStreams)
   stream.on('data', (entry) => {