diff --git a/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java b/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java
index 3422b2978e..248de665eb 100644
--- a/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java
+++ b/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java
@@ -490,6 +490,7 @@ public final class CraftServer implements Server {
         if (type == PluginLoadOrder.STARTUP) {
             this.helpMap.clear();
             this.helpMap.initializeGeneralTopics();
+            if (io.papermc.paper.configuration.GlobalConfiguration.get().misc.loadPermissionsYmlBeforePlugins) loadCustomPermissions(); // Paper
         }
 
         Plugin[] plugins = this.pluginManager.getPlugins();
@@ -509,7 +510,7 @@ public final class CraftServer implements Server {
             this.commandMap.registerServerAliases();
             DefaultPermissions.registerCorePermissions();
             CraftDefaultPermissions.registerCorePermissions();
-            this.loadCustomPermissions();
+            if (!io.papermc.paper.configuration.GlobalConfiguration.get().misc.loadPermissionsYmlBeforePlugins) this.loadCustomPermissions(); // Paper
             this.helpMap.initializeCommands();
             this.syncCommands();
         }