diff --git a/src/interface/obsidian/src/main.ts b/src/interface/obsidian/src/main.ts
index 65dac069..1fbed55f 100644
--- a/src/interface/obsidian/src/main.ts
+++ b/src/interface/obsidian/src/main.ts
@@ -59,7 +59,9 @@ export default class Khoj extends Plugin {
         // Add scheduled job to update index every 60 minutes
         this.indexingTimer = setInterval(async () => {
             if (this.settings.autoConfigure) {
-                this.lastSyncedFiles = await updateContentIndex(this.app.vault, this.settings);
+                this.settings.lastSyncedFiles = await updateContentIndex(
+                    this.app.vault, this.settings, this.settings.lastSyncedFiles
+                );
             }
         }, 60 * 60 * 1000);
     }
diff --git a/src/interface/obsidian/src/settings.ts b/src/interface/obsidian/src/settings.ts
index c013f10c..dfb6e6bb 100644
--- a/src/interface/obsidian/src/settings.ts
+++ b/src/interface/obsidian/src/settings.ts
@@ -1,4 +1,4 @@
-import { App, Notice, PluginSettingTab, request, Setting } from 'obsidian';
+import { App, Notice, PluginSettingTab, request, Setting, TFile } from 'obsidian';
 import Khoj from 'src/main';
 
 export interface KhojSetting {
@@ -8,6 +8,7 @@ export interface KhojSetting {
     khojUrl: string;
     connectedToBackend: boolean;
     autoConfigure: boolean;
+    lastSyncedFiles: TFile[];
 }
 
 export const DEFAULT_SETTINGS: KhojSetting = {
@@ -17,6 +18,7 @@ export const DEFAULT_SETTINGS: KhojSetting = {
     connectedToBackend: false,
     autoConfigure: true,
     openaiApiKey: '',
+    lastSyncedFiles: []
 }
 
 export class KhojSettingTab extends PluginSettingTab {
diff --git a/src/interface/obsidian/src/utils.ts b/src/interface/obsidian/src/utils.ts
index 1707703a..9dba9fb9 100644
--- a/src/interface/obsidian/src/utils.ts
+++ b/src/interface/obsidian/src/utils.ts
@@ -41,21 +41,32 @@ function fileExtensionToMimeType (extension: string): string {
     }
 }
 
-export async function updateContentIndex(vault: Vault, setting: KhojSetting): Promise<TFile[]> {
+export async function updateContentIndex(vault: Vault, setting: KhojSetting, lastSyncedFiles: TFile[]): Promise<TFile[]> {
     // Get all markdown, pdf files in the vault
     console.log(`Khoj: Updating Khoj content index...`)
     const files = vault.getFiles().filter(file => file.extension === 'md' || file.extension === 'pdf');
     const binaryFileTypes = ['pdf', 'png', 'jpg', 'jpeg']
+    let countOfFilesToIndex = 0;
+    let countOfFilesToDelete = 0;
 
-    // Create multipart form data with all markdown, pdf files
+    // Add all files to index as multipart form data
     const formData = new FormData();
     for (const file of files) {
+        countOfFilesToIndex++;
         const encoding = binaryFileTypes.includes(file.extension) ? "binary" : "utf8";
         const mimeType = fileExtensionToMimeType(file.extension) + (encoding === "utf8" ? "; charset=UTF-8" : "");
         const fileContent = await vault.read(file);
         formData.append('files', new Blob([fileContent], { type: mimeType }), file.path);
     }
 
+    // Add any previously synced files to be deleted to multipart form data
+    for (const lastSyncedFile of lastSyncedFiles) {
+        if (!files.includes(lastSyncedFile)) {
+            countOfFilesToDelete++;
+            formData.append('files', new Blob([]), lastSyncedFile.path);
+        }
+    }
+
     // Call Khoj backend to update index with all markdown, pdf files
     const response = await fetch(`${setting.khojUrl}/api/v1/indexer/batch`, {
         method: 'POST',
@@ -68,7 +79,7 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting): Pr
     if (!response.ok) {
         new Notice(`❗️Failed to update Khoj content index. Ensure Khoj server connected or raise issue on Khoj Discord/Github\nError: ${response.statusText}`);
     } else {
-        console.log(`✅ Refreshed Khoj content index.`);
+        console.log(`✅ Refreshed Khoj content index. Updated: ${countOfFilesToIndex} files, Deleted: ${countOfFilesToDelete} files.`);
     }
 
     return files;