diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt
index c715e0604..9ce4ecd3e 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt
@@ -1,7 +1,9 @@
 package eu.kanade.tachiyomi.data.download
 
 import android.content.Context
+import android.util.AtomicFile
 import androidx.core.net.toUri
+import androidx.core.util.writeBytes
 import com.hippo.unifile.UniFile
 import dev.zacsweers.metro.AppScope
 import dev.zacsweers.metro.Inject
@@ -25,7 +27,6 @@ import kotlinx.coroutines.flow.onStart
 import kotlinx.coroutines.flow.receiveAsFlow
 import kotlinx.coroutines.flow.shareIn
 import kotlinx.coroutines.flow.stateIn
-import kotlinx.coroutines.launch
 import kotlinx.coroutines.sync.Mutex
 import kotlinx.coroutines.sync.withLock
 import kotlinx.coroutines.withTimeoutOrNull
@@ -88,25 +89,26 @@ class DownloadCache(
      */
     private var lastRenew = 0L
     private var renewalJob: Job? = null
+    private val initJob: Job
 
     private val _isInitializing = MutableStateFlow(false)
     val isInitializing = _isInitializing
         .debounce(1.seconds) // Don't notify if it finishes quickly enough
         .stateIn(scope, SharingStarted.WhileSubscribed(), false)
 
-    private val diskCacheFile: File
-        get() = File(context.cacheDir, "dl_index_cache_v3")
+    private val diskCacheFile: AtomicFile
+        get() = AtomicFile(File(context.cacheDir, "dl_index_cache_v3"))
 
     private val rootDownloadsDirMutex = Mutex()
     private var rootDownloadsDir = RootDirectory(storageManager.getDownloadsDirectory())
 
     init {
         // Attempt to read cache file
-        scope.launch {
+        initJob = scope.launchIO {
             rootDownloadsDirMutex.withLock {
                 try {
-                    if (diskCacheFile.exists()) {
-                        val diskCache = diskCacheFile.inputStream().use {
+                    if (diskCacheFile.baseFile.exists()) {
+                        val diskCache = diskCacheFile.openRead().use {
                             ProtoBuf.decodeFromByteArray<RootDirectory>(it.readBytes())
                         }
                         rootDownloadsDir = diskCache
@@ -360,6 +362,9 @@ class DownloadCache(
         }
 
         renewalJob = scope.launchIO {
+            // The disk index is older than this scan and would replace it if read afterwards
+            initJob.join()
+
             if (lastRenew == 0L) {
                 _isInitializing.emit(true)
             }
@@ -445,8 +450,9 @@ class DownloadCache(
         updateDiskCacheJob?.cancel()
         updateDiskCacheJob = scope.launchIO {
             delay(1.seconds)
-            ensureActive()
-            val bytes = ProtoBuf.encodeToByteArray(rootDownloadsDir)
+            val bytes = rootDownloadsDirMutex.withLock {
+                ProtoBuf.encodeToByteArray(rootDownloadsDir)
+            }
             ensureActive()
             try {
                 diskCacheFile.writeBytes(bytes)