diff --git a/controller/src/classes/Controller.ts b/controller/src/classes/Controller.ts
index 5b2d343..753ddd9 100644
--- a/controller/src/classes/Controller.ts
+++ b/controller/src/classes/Controller.ts
@@ -195,15 +195,33 @@ export class Controller<T extends Record<keyof T, BaseSubject<keyof T & string>>
         const configs: SubjectConfig<T>[] = Object.values(this.subjectConfigs);
 
         const index = await this.store.getCurrentIndex();
-        const resourcesToSkip = index.items.filter(i => i.resource.includes(containerUrl));
+        const resourcesToSkip = index.items.filter(i => {
+            if (!i.resource.includes(containerUrl)) {
+                return false;
+            }
+            const strippedURI = i.resource.replace(containerUrl, "");
+            const slashIdx = strippedURI.indexOf("/");
+            if (slashIdx < 0) {
+                return true;
+            }
+            return !strippedURI.includes("/", slashIdx + 1)
+        });
 
         const results = await Promise.allSettled(configs.map(c => c.manager.getContainerPermissionList(containerUrl, resourcesToSkip.map(i => i.resource))))
+        const resourcesToClean = resourcesToSkip.filter(r => r.isEnabled).map(r => r.resource);
 
         if (results.length !== 0) {
             index.items.push(...results.reduce<IndexItem<T[SubjectKey<T>]>[]>((arr, v) => {
                 if (v.status === "fulfilled") {
                     // Check if the resourceUrl is already present before pushing it into the array
                     v.value.forEach((r) => {
+                        for (let i = 0; i < resourcesToClean.length; i++) {
+                            const rtc = resourcesToClean[i];
+                            if (r.resourceUrl.includes(rtc)) {
+                                resourcesToClean.splice(i, 1);
+                                i--;
+                            }
+                        }
                         // @ts-expect-error
                         arr.push(...r.permissionsPerSubject.map(p => ({
                             id: crypto.randomUUID(),
@@ -217,10 +235,19 @@ export class Controller<T extends Record<keyof T, BaseSubject<keyof T & string>>
                 }
                 return arr;
             }, []));
-
-            await this.store.saveToRemoteIndex();
         }
 
+        await Promise.allSettled(resourcesToClean.map(async r => {
+            for (let i = 0; i < index.items.length; i++) {
+                let entry = index.items[i];
+                if (!entry.resource.includes(r)) {
+                    continue
+                }
+                index.items.splice(i, 1);
+            }
+        }));
+
+        await this.store.saveToRemoteIndex();
 
         return index.items.reduce<ResourcePermissions<T[keyof T]>[]>((arr, v) => {
             const resourcePath = v.resource.replace(containerUrl, "");
diff --git a/controller/src/classes/permissionManager/inrupt/InruptPermissionManager.ts b/controller/src/classes/permissionManager/inrupt/InruptPermissionManager.ts
index e063dc4..1d9bf12 100644
--- a/controller/src/classes/permissionManager/inrupt/InruptPermissionManager.ts
+++ b/controller/src/classes/permissionManager/inrupt/InruptPermissionManager.ts
@@ -83,11 +83,18 @@ export abstract class InruptPermissionManager<T extends Record<keyof T, BaseSubj
         const dataset = await getSolidDataset(containerUrl, { fetch: session.fetch });
         const results = await Promise.allSettled(
             getThingAll(dataset)
-                .filter(r => !resourceToSkip?.includes(r.url))
-                .map(async (resource) => ({
-                    resourceUrl: resource.url,
-                    permissionsPerSubject: await this.getRemotePermissions(resource.url)
-                }))
+                .map(async (resource) => {
+                    if (resourceToSkip.includes(resource.url)) {
+                        return {
+                            resourceUrl: resource.url,
+                            permissionsPerSubject: [],
+                        }
+                    }
+                    return {
+                        resourceUrl: resource.url,
+                        permissionsPerSubject: await this.getRemotePermissions(resource.url)
+                    }
+                })
         )
         return results.reduce<ResourcePermissions<T[keyof T]>[]>((arr, v) => {
             if (v.status == "fulfilled") {
diff --git a/controller/src/types/modules.ts b/controller/src/types/modules.ts
index 47d3019..f299986 100644
--- a/controller/src/types/modules.ts
+++ b/controller/src/types/modules.ts
@@ -77,7 +77,9 @@ export interface IPermissionManager<T = Record<string, BaseSubject<string>>> {
     deletePermissions<K extends SubjectKey<T>>(resource: string, subject: T[K]): Promise<void>
     getRemotePermissions<K extends SubjectKey<T>>(resourceUrl: string): Promise<SubjectPermissions<T[K]>[]>
     /**
-    * Retrieve the permissions of the resources  in this  container.
+    * Retrieve the permissions of the resources in this container.
+    * It will add the skipped resources to the returning object but without the permissions assignments.
+    * As this is necessary to clean-up the index
     * Will probably work for a resource, but not guaranteed. Use getRemotePermissions for that
     */
     getContainerPermissionList(containerUrl: string, resourceToSkip?: string[]): Promise<ResourcePermissions<T[keyof T]>[]>