diff --git a/.changeset/new-swans-heal.md b/.changeset/new-swans-heal.md
new file mode 100644
index 000000000..1778913a8
--- /dev/null
+++ b/.changeset/new-swans-heal.md
@@ -0,0 +1,5 @@
+---
+"@tanstack/db": patch
+---
+
+fix a race condition that could result in the initial state of a joined collection being sent to the live query pipeline twice, this would result in incorrect join results.
diff --git a/packages/db/src/query/live/collection-subscriber.ts b/packages/db/src/query/live/collection-subscriber.ts
index 07fe577ff..03dfb63f1 100644
--- a/packages/db/src/query/live/collection-subscriber.ts
+++ b/packages/db/src/query/live/collection-subscriber.ts
@@ -113,6 +113,7 @@ export class CollectionSubscriber<
           // filter out deletes for keys that have not been sent
           continue
         }
+        this.sentKeys.add(change.key)
       }
       newChanges.push(newChange)
     }
@@ -153,12 +154,29 @@ export class CollectionSubscriber<
   private subscribeToMatchingChanges(
     whereExpression: BasicExpression<boolean> | undefined
   ) {
+    // Flag to indicate we have send to whole initial state of the collection
+    // to the pipeline, this is set when there are no indexes that can be used
+    // to filter the changes and so the whole state was requested from the collection
     let loadedInitialState = false
 
+    // Flag to indicate that we have started sending changes to the pipeline.
+    // This is set to true by either the first call to `loadKeys` or when the
+    // query requests the whole initial state in `loadInitialState`.
+    // Until that point we filter out all changes from subscription to the collection.
+    let sendChanges = false
+
     const sendVisibleChanges = (
       changes: Array<ChangeMessage<any, string | number>>
     ) => {
-      this.sendVisibleChangesToPipeline(changes, loadedInitialState)
+      // We filter out changes when sendChanges is false to ensure that we don't send
+      // any changes from the live subscription until the join operator requests either
+      // the initial state or its first key. This is needed otherwise it could receive
+      // changes which are then later subsumed by the initial state (and that would
+      // lead to weird bugs due to the data being received twice).
+      this.sendVisibleChangesToPipeline(
+        sendChanges ? changes : [],
+        loadedInitialState
+      )
     }
 
     const unsubscribe = this.collection.subscribeChanges(sendVisibleChanges, {
@@ -171,6 +189,7 @@ export class CollectionSubscriber<
       ? createFilterFunctionFromExpression(whereExpression)
       : () => true
     const loadKs = (keys: Set<string | number>) => {
+      sendChanges = true
       return this.loadKeys(keys, filterFn)
     }
 
@@ -183,6 +202,7 @@ export class CollectionSubscriber<
         // Make sure we only load the initial state once
         if (loadedInitialState) return
         loadedInitialState = true
+        sendChanges = true
 
         const changes = this.collection.currentStateAsChanges({
           whereExpression,
diff --git a/packages/db/tests/query/live-query-collection.test.ts b/packages/db/tests/query/live-query-collection.test.ts
index 7fb59dc3a..2570c0812 100644
--- a/packages/db/tests/query/live-query-collection.test.ts
+++ b/packages/db/tests/query/live-query-collection.test.ts
@@ -2,7 +2,10 @@ import { beforeEach, describe, expect, it } from "vitest"
 import { createCollection } from "../../src/collection.js"
 import { createLiveQueryCollection, eq } from "../../src/query/index.js"
 import { Query } from "../../src/query/builder/index.js"
-import { mockSyncCollectionOptions } from "../utls.js"
+import {
+  mockSyncCollectionOptions,
+  mockSyncCollectionOptionsNoInitialState,
+} from "../utls.js"
 import type { ChangeMessage } from "../../src/types.js"
 
 // Sample user type for tests
@@ -313,4 +316,92 @@ describe(`createLiveQueryCollection`, () => {
     // Resubscribe should not throw (would throw "Graph already finalized" without the fix)
     expect(() => liveQuery.subscribeChanges(() => {})).not.toThrow()
   })
+
+  for (const autoIndex of [`eager`, `off`] as const) {
+    it(`should not send the initial state twice on joins with autoIndex: ${autoIndex}`, async () => {
+      type Player = { id: number; name: string }
+      type Challenge = { id: number; value: number }
+
+      const playerCollection = createCollection(
+        mockSyncCollectionOptionsNoInitialState<Player>({
+          id: `player`,
+          getKey: (post) => post.id,
+          autoIndex,
+        })
+      )
+
+      const challenge1Collection = createCollection(
+        mockSyncCollectionOptionsNoInitialState<Challenge>({
+          id: `challenge1`,
+          getKey: (post) => post.id,
+          autoIndex,
+        })
+      )
+
+      const challenge2Collection = createCollection(
+        mockSyncCollectionOptionsNoInitialState<Challenge>({
+          id: `challenge2`,
+          getKey: (post) => post.id,
+          autoIndex,
+        })
+      )
+
+      const liveQuery = createLiveQueryCollection((q) =>
+        q
+          .from({ player: playerCollection })
+          .leftJoin(
+            { challenge1: challenge1Collection },
+            ({ player, challenge1 }) => eq(player.id, challenge1.id)
+          )
+          .leftJoin(
+            { challenge2: challenge2Collection },
+            ({ player, challenge2 }) => eq(player.id, challenge2.id)
+          )
+      )
+
+      // Start the query, but don't wait it, we are doing to write the data to the
+      // source collections while the query is loading the initial state
+      const preloadPromise = liveQuery.preload()
+
+      // Write player
+      playerCollection.utils.begin()
+      playerCollection.utils.write({
+        type: `insert`,
+        value: { id: 1, name: `Alice` },
+      })
+      playerCollection.utils.commit()
+      playerCollection.utils.markReady()
+
+      // Write challenge1
+      challenge1Collection.utils.begin()
+      challenge1Collection.utils.write({
+        type: `insert`,
+        value: { id: 1, value: 100 },
+      })
+      challenge1Collection.utils.commit()
+      challenge1Collection.utils.markReady()
+
+      // Write challenge2
+      challenge2Collection.utils.begin()
+      challenge2Collection.utils.write({
+        type: `insert`,
+        value: { id: 1, value: 200 },
+      })
+      challenge2Collection.utils.commit()
+      challenge2Collection.utils.markReady()
+
+      await preloadPromise
+
+      // With a failed test the results show more than 1 item
+      // It returns both an unjoined player with no joined challenges, and a joined
+      // player with the challenges
+      const results = liveQuery.toArray
+      expect(results.length).toBe(1)
+
+      const result = results[0]!
+      expect(result.player.name).toBe(`Alice`)
+      expect(result.challenge1?.value).toBe(100)
+      expect(result.challenge2?.value).toBe(200)
+    })
+  }
 })
diff --git a/packages/db/tests/utls.ts b/packages/db/tests/utls.ts
index 9ab74d3a5..6fb4aae0e 100644
--- a/packages/db/tests/utls.ts
+++ b/packages/db/tests/utls.ts
@@ -5,13 +5,6 @@ import type {
   SyncConfig,
 } from "../src/index.js"
 
-type MockSyncCollectionConfig<T> = {
-  id: string
-  initialData: Array<T>
-  getKey: (item: T) => string | number
-  autoIndex?: `off` | `eager`
-}
-
 // Index usage tracking utilities
 export interface IndexUsageStats {
   rangeQueryCalls: number
@@ -179,6 +172,13 @@ export function withIndexTracking(
   }
 }
 
+type MockSyncCollectionConfig<T> = {
+  id: string
+  initialData: Array<T>
+  getKey: (item: T) => string | number
+  autoIndex?: `off` | `eager`
+}
+
 export function mockSyncCollectionOptions<
   T extends object = Record<string, unknown>,
 >(config: MockSyncCollectionConfig<T>) {
@@ -257,3 +257,80 @@ export function mockSyncCollectionOptions<
 
   return options
 }
+
+type MockSyncCollectionConfigNoInitialState<T> = {
+  id: string
+  getKey: (item: T) => string | number
+  autoIndex?: `off` | `eager`
+}
+
+export function mockSyncCollectionOptionsNoInitialState<
+  T extends object = Record<string, unknown>,
+>(config: MockSyncCollectionConfigNoInitialState<T>) {
+  let begin: () => void
+  let write: Parameters<SyncConfig<T>[`sync`]>[0][`write`]
+  let commit: () => void
+  let markReady: () => void
+
+  let syncPendingPromise: Promise<void> | undefined
+  let syncPendingResolve: (() => void) | undefined
+  let syncPendingReject: ((error: Error) => void) | undefined
+
+  const awaitSync = async () => {
+    if (syncPendingPromise) {
+      return syncPendingPromise
+    }
+    syncPendingPromise = new Promise((resolve, reject) => {
+      syncPendingResolve = resolve
+      syncPendingReject = reject
+    })
+    syncPendingPromise.then(() => {
+      syncPendingPromise = undefined
+      syncPendingResolve = undefined
+      syncPendingReject = undefined
+    })
+    return syncPendingPromise
+  }
+
+  const utils = {
+    begin: () => begin!(),
+    write: ((value) => write!(value)) as typeof write,
+    commit: () => commit!(),
+    markReady: () => markReady!(),
+    resolveSync: () => {
+      syncPendingResolve!()
+    },
+    rejectSync: (error: Error) => {
+      syncPendingReject!(error)
+    },
+  }
+
+  const options: CollectionConfig<T> & { utils: typeof utils } = {
+    sync: {
+      sync: (params: Parameters<SyncConfig<T>[`sync`]>[0]) => {
+        begin = params.begin
+        write = params.write
+        commit = params.commit
+        markReady = params.markReady
+      },
+    },
+    startSync: false,
+    onInsert: async (_params: MutationFnParams<T>) => {
+      // TODO
+      await awaitSync()
+    },
+    onUpdate: async (_params: MutationFnParams<T>) => {
+      // TODO
+      await awaitSync()
+    },
+    onDelete: async (_params: MutationFnParams<T>) => {
+      // TODO
+      await awaitSync()
+    },
+    utils,
+    ...config,
+    autoIndex: config.autoIndex,
+  }
+
+  return options
+}