diff --git a/plugin/src/main/java/com/denizenscript/denizen/Denizen.java b/plugin/src/main/java/com/denizenscript/denizen/Denizen.java
index 8b0cde8da0..067181fe0d 100644
--- a/plugin/src/main/java/com/denizenscript/denizen/Denizen.java
+++ b/plugin/src/main/java/com/denizenscript/denizen/Denizen.java
@@ -29,6 +29,7 @@
 import com.denizenscript.denizen.utilities.debugging.Debug;
 import com.denizenscript.denizen.utilities.depends.Depends;
 import com.denizenscript.denizen.utilities.entity.DenizenEntityType;
+import com.denizenscript.denizen.utilities.flags.DataPersistenceFlagTracker;
 import com.denizenscript.denizen.utilities.flags.PlayerFlagHandler;
 import com.denizenscript.denizen.utilities.implementation.DenizenCoreImplementation;
 import com.denizenscript.denizen.utilities.maps.DenizenMapManager;
@@ -41,6 +42,7 @@
 import com.denizenscript.denizen.npc.DenizenNPCHelper;
 import com.denizenscript.denizencore.DenizenCore;
 import com.denizenscript.denizencore.events.OldEventManager;
+import com.denizenscript.denizencore.flags.MapTagBasedFlagTracker;
 import com.denizenscript.denizencore.flags.SavableMapFlagTracker;
 import com.denizenscript.denizencore.objects.ObjectFetcher;
 import com.denizenscript.denizencore.scripts.ScriptHelper;
@@ -51,9 +53,7 @@
 import com.denizenscript.denizencore.utilities.debugging.SlowWarning;
 import com.denizenscript.denizencore.utilities.debugging.StrongWarning;
 import com.denizenscript.denizencore.utilities.text.ConfigUpdater;
-import org.bukkit.Bukkit;
-import org.bukkit.ChatColor;
-import org.bukkit.OfflinePlayer;
+import org.bukkit.*;
 import org.bukkit.command.Command;
 import org.bukkit.command.CommandSender;
 import org.bukkit.configuration.file.FileConfiguration;
@@ -415,6 +415,13 @@ public void run() {
                         }
                     }, 1, 1);
                     InventoryTag.setupInventoryTracker();
+                    if (!MapTagBasedFlagTracker.skipAllCleanings) {
+                        for (World world : Bukkit.getWorlds()) {
+                            for (Chunk chunk : world.getLoadedChunks()) {
+                                new DataPersistenceFlagTracker(chunk).doTotalClean();
+                            }
+                        }
+                    }
                 }
                 catch (Exception e) {
                     Debug.echoError(e);
diff --git a/plugin/src/main/java/com/denizenscript/denizen/npc/traits/DenizenFlagsTrait.java b/plugin/src/main/java/com/denizenscript/denizen/npc/traits/DenizenFlagsTrait.java
index b17422a8c2..c0ee1d0f92 100644
--- a/plugin/src/main/java/com/denizenscript/denizen/npc/traits/DenizenFlagsTrait.java
+++ b/plugin/src/main/java/com/denizenscript/denizen/npc/traits/DenizenFlagsTrait.java
@@ -25,6 +25,7 @@ public SavableMapFlagTracker create(DataKey dataKey) {
             for (DataKey key : dataKey.getSubKeys()) {
                 toRet.setRootMap(key.name(), MapTag.valueOf(key.getString(""), CoreUtilities.errorButNoDebugContext));
             }
+            toRet.doTotalClean();
             return toRet;
         }
 
diff --git a/plugin/src/main/java/com/denizenscript/denizen/objects/EntityTag.java b/plugin/src/main/java/com/denizenscript/denizen/objects/EntityTag.java
index 25e98099c2..ec85d8d03e 100644
--- a/plugin/src/main/java/com/denizenscript/denizen/objects/EntityTag.java
+++ b/plugin/src/main/java/com/denizenscript/denizen/objects/EntityTag.java
@@ -13,6 +13,7 @@
 import com.denizenscript.denizen.utilities.entity.FakeEntity;
 import com.denizenscript.denizen.utilities.flags.DataPersistenceFlagTracker;
 import com.denizenscript.denizen.utilities.nbt.CustomNBT;
+import com.denizenscript.denizencore.DenizenCore;
 import com.denizenscript.denizencore.flags.AbstractFlagTracker;
 import com.denizenscript.denizencore.flags.FlaggableObject;
 import com.denizenscript.denizencore.objects.*;
@@ -427,10 +428,14 @@ public AbstractFlagTracker getFlagTracker() {
 
     @Override
     public void reapplyTracker(AbstractFlagTracker tracker) {
-        // Nothing to do.
+        if (cleanRateProtect + 60000 > DenizenCore.serverTimeMillis) {
+            ((DataPersistenceFlagTracker) tracker).doTotalClean();
+            cleanRateProtect = DenizenCore.serverTimeMillis;
+        }
     }
 
     public Entity entity = null;
+    public long cleanRateProtect = -60000;
     public DenizenEntityType entity_type = null;
     private String data1 = null;
     private DespawnedEntity despawned_entity = null;
diff --git a/plugin/src/main/java/com/denizenscript/denizen/scripts/containers/core/BukkitWorldScriptHelper.java b/plugin/src/main/java/com/denizenscript/denizen/scripts/containers/core/BukkitWorldScriptHelper.java
index 55a5473296..a3444d2c61 100644
--- a/plugin/src/main/java/com/denizenscript/denizen/scripts/containers/core/BukkitWorldScriptHelper.java
+++ b/plugin/src/main/java/com/denizenscript/denizen/scripts/containers/core/BukkitWorldScriptHelper.java
@@ -7,6 +7,8 @@
 import com.denizenscript.denizen.utilities.ScoreboardHelper;
 import com.denizenscript.denizen.utilities.debugging.Debug;
 import com.denizenscript.denizen.utilities.Settings;
+import com.denizenscript.denizen.utilities.flags.DataPersistenceFlagTracker;
+import com.denizenscript.denizencore.flags.MapTagBasedFlagTracker;
 import org.bukkit.Bukkit;
 import org.bukkit.ChatColor;
 import org.bukkit.World;
@@ -17,6 +19,7 @@
 import org.bukkit.event.player.PlayerJoinEvent;
 import org.bukkit.event.player.PlayerLoginEvent;
 import org.bukkit.event.player.PlayerQuitEvent;
+import org.bukkit.event.world.ChunkLoadEvent;
 import org.bukkit.scoreboard.Scoreboard;
 
 import java.util.HashMap;
@@ -109,4 +112,12 @@ public void playerLogin(PlayerLoginEvent event) {
     public void playerQuit(PlayerQuitEvent event) {
         NMSHandler.getPacketHelper().removeNoCollideTeam(event.getPlayer(), null);
     }
+
+    @EventHandler
+    public void chunkLoadEvent(ChunkLoadEvent event) {
+        if (MapTagBasedFlagTracker.skipAllCleanings) {
+            return;
+        }
+        new DataPersistenceFlagTracker(event.getChunk()).doTotalClean();
+    }
 }
diff --git a/plugin/src/main/java/com/denizenscript/denizen/utilities/Settings.java b/plugin/src/main/java/com/denizenscript/denizen/utilities/Settings.java
index 6946e82020..8986e4954c 100644
--- a/plugin/src/main/java/com/denizenscript/denizen/utilities/Settings.java
+++ b/plugin/src/main/java/com/denizenscript/denizen/utilities/Settings.java
@@ -2,6 +2,7 @@
 
 import com.denizenscript.denizen.Denizen;
 import com.denizenscript.denizen.utilities.flags.PlayerFlagHandler;
+import com.denizenscript.denizencore.flags.MapTagBasedFlagTracker;
 import com.denizenscript.denizencore.utilities.debugging.Debug;
 import com.denizenscript.denizencore.objects.core.DurationTag;
 import com.denizenscript.denizencore.scripts.ScriptHelper;
@@ -87,6 +88,7 @@ public static void refillCache() {
         cache_packetInterception = config.getBoolean("Packets.Interception", true);
         PlayerFlagHandler.cacheTimeoutSeconds = config.getLong("Saves.Offline player cache timeout", 300);
         PlayerFlagHandler.asyncPreload = config.getBoolean("Saves.Load async on login", true);
+        MapTagBasedFlagTracker.skipAllCleanings = config.getBoolean("Saves.Skip flag cleaning", false);
     }
 
     private static boolean cache_showDebug = true, cache_overrideHelp, cache_useDefaultScriptPath,
diff --git a/plugin/src/main/java/com/denizenscript/denizen/utilities/flags/DataPersistenceFlagTracker.java b/plugin/src/main/java/com/denizenscript/denizen/utilities/flags/DataPersistenceFlagTracker.java
index 5e5625fa1c..391fae3b40 100644
--- a/plugin/src/main/java/com/denizenscript/denizen/utilities/flags/DataPersistenceFlagTracker.java
+++ b/plugin/src/main/java/com/denizenscript/denizen/utilities/flags/DataPersistenceFlagTracker.java
@@ -2,8 +2,10 @@
 
 import com.denizenscript.denizen.utilities.DataPersistenceHelper;
 import com.denizenscript.denizencore.flags.MapTagBasedFlagTracker;
+import com.denizenscript.denizencore.objects.ObjectTag;
 import com.denizenscript.denizencore.objects.core.MapTag;
 import com.denizenscript.denizencore.utilities.CoreUtilities;
+import org.bukkit.NamespacedKey;
 import org.bukkit.persistence.PersistentDataHolder;
 
 import java.util.Collection;
@@ -44,4 +46,29 @@ public Collection<String> listAllFlags() {
                 .filter(k -> k.getNamespace().equals("denizen") && k.getKey().startsWith(keyPrefix))
                 .map(k -> k.getKey().substring(keyPrefix.length())).collect(Collectors.toList());
     }
+
+    public void doTotalClean() {
+        if (MapTagBasedFlagTracker.skipAllCleanings) {
+            return;
+        }
+        for (NamespacedKey key : holder.getPersistentDataContainer().getKeys()) {
+            if (!key.getNamespace().equals("denizen") || !key.getKey().startsWith("flag_")) {
+                continue;
+            }
+            ObjectTag map = holder.getPersistentDataContainer().get(key, DataPersistenceHelper.PERSISTER_TYPE);
+            if (!(map instanceof MapTag)) {
+                continue;
+            }
+            if (isExpired(((MapTag) map).map.get(expirationString))) {
+                holder.getPersistentDataContainer().remove(key);
+                continue;
+            }
+            ObjectTag subValue = ((MapTag) map).map.get(valueString);
+            if (subValue instanceof MapTag) {
+                if (doClean((MapTag) subValue)) {
+                    holder.getPersistentDataContainer().set(key, DataPersistenceHelper.PERSISTER_TYPE, map);
+                }
+            }
+        }
+    }
 }
diff --git a/plugin/src/main/resources/config.yml b/plugin/src/main/resources/config.yml
index 65206b0809..1b7f3ec48f 100644
--- a/plugin/src/main/resources/config.yml
+++ b/plugin/src/main/resources/config.yml
@@ -184,6 +184,9 @@ Saves:
   Offline player cache timeout: 300
   # When set to 'true', player data will be loaded offthread during the login sequence, to avoid adding load to the server while players join.
   Load async on login: true
+  # When set to 'true', all automatic flag cleanups will be skipped.
+  # This might save some processing time on servers that rarely use flag expirations, but otherwise should be left as 'false'.
+  Skip flag cleaning: false
 
 Packets:
   # Whether to allow Denizen to intercept packets from and to player clients.