diff --git a/src/service/github.service.ts b/src/service/github.service.ts
index c9c2221d..bcfa17d3 100644
--- a/src/service/github.service.ts
+++ b/src/service/github.service.ts
@@ -184,6 +184,21 @@ export class GitHubService {
     return gistObject;
   }
 
+  public UpdateChangedFiles(
+    gistObject: any,
+    files: File[],
+    deletedFileNames: string[]
+  ): any {
+    gistObject.data.files = {};
+    gistObject.data = this.AddFile(files, gistObject.data);
+
+    for (const fileName of deletedFileNames) {
+      gistObject.data.files[fileName] = null;
+    }
+
+    return gistObject;
+  }
+
   public async SaveGIST(gistObject: any): Promise<boolean> {
     gistObject.gist_id = gistObject.id;
     // tslint:disable-next-line:comment-format
diff --git a/src/sync.ts b/src/sync.ts
index 3e926481..afd097bc 100644
--- a/src/sync.ts
+++ b/src/sync.ts
@@ -228,6 +228,7 @@ export class Sync {
       let completed: boolean = false;
 
       let newGIST: boolean = false;
+      let uploadedSettingFiles: File[] = allSettingFiles;
       try {
         if (syncSetting.gist == null || syncSetting.gist === "") {
           if (customSettings.askGistDescription) {
@@ -284,23 +285,39 @@ export class Sync {
           localConfig.publicGist = true;
         }
 
-        if (
-          !allSettingFiles.some(fileToUpload => {
-            if (fileToUpload.gistName === "cloudSettings") {
+        const cloudSettingsFile = allSettingFiles.find(
+          fileToUpload => fileToUpload.gistName === "cloudSettings"
+        );
+        const changedSettingFiles = allSettingFiles.filter(fileToUpload => {
+          if (fileToUpload.gistName === "cloudSettings") {
+            return false;
+          }
+          if (!gistObj.data.files[fileToUpload.gistName]) {
+            return true;
+          }
+          if (
+            gistObj.data.files[fileToUpload.gistName].content !==
+            fileToUpload.content
+          ) {
+            console.info(`Sync: file ${fileToUpload.gistName} has changed`);
+            return true;
+          }
+          return false;
+        });
+        const deletedGistFileNames = Object.keys(gistObj.data.files).filter(
+          gistFileName => {
+            if (gistFileName.startsWith("keybindings")) {
               return false;
             }
-            if (!gistObj.data.files[fileToUpload.gistName]) {
-              return true;
-            }
-            if (
-              gistObj.data.files[fileToUpload.gistName].content !==
-              fileToUpload.content
-            ) {
-              console.info(`Sync: file ${fileToUpload.gistName} has changed`);
-              return true;
-            }
-          })
-        ) {
+            return !allSettingFiles.some(
+              fileToUpload => fileToUpload.gistName === gistFileName
+            );
+          }
+        );
+        const hasSettingChanges =
+          changedSettingFiles.length > 0 || deletedGistFileNames.length > 0;
+
+        if (!hasSettingChanges) {
           // Gist files are the same as the local files.
           if (!localConfig.extConfig.forceUpload) {
             vscode.window.setStatusBarMessage(
@@ -359,7 +376,18 @@ export class Sync {
           3000
         );
 
-        gistObj = github.UpdateGIST(gistObj, allSettingFiles);
+        if (!newGIST && !localConfig.extConfig.forceUpload) {
+          uploadedSettingFiles = cloudSettingsFile
+            ? [...changedSettingFiles, cloudSettingsFile]
+            : changedSettingFiles;
+          gistObj = github.UpdateChangedFiles(
+            gistObj,
+            uploadedSettingFiles,
+            deletedGistFileNames
+          );
+        } else {
+          gistObj = github.UpdateGIST(gistObj, allSettingFiles);
+        }
         completed = await github.SaveGIST(gistObj.data);
         if (!completed) {
           vscode.window.showErrorMessage(
@@ -396,7 +424,7 @@ export class Sync {
           if (!syncSetting.quietSync) {
             state.commons.ShowSummaryOutput(
               true,
-              allSettingFiles,
+              uploadedSettingFiles,
               null,
               uploadedExtensions,
               ignoredExtensions,
diff --git a/test/service/githubService/githubService.test.ts b/test/service/githubService/githubService.test.ts
new file mode 100644
index 00000000..be27d2e3
--- /dev/null
+++ b/test/service/githubService/githubService.test.ts
@@ -0,0 +1,63 @@
+import { expect } from "chai";
+
+import { File } from "../../../src/service/file.service";
+import { GitHubService } from "../../../src/service/github.service";
+
+describe("GitHubService", () => {
+  it("should update only changed files", () => {
+    const github: GitHubService = Object.create(GitHubService.prototype);
+    const gistObject = {
+      data: {
+        files: {
+          "extensions.json": {
+            content: "unchanged"
+          },
+          "settings.json": {
+            content: "old"
+          }
+        }
+      }
+    };
+
+    const actual = github.UpdateChangedFiles(
+      gistObject,
+      [new File("settings.json", "new", "", "settings.json")],
+      []
+    );
+
+    expect(actual.data.files).to.deep.equals({
+      "settings.json": {
+        content: "new"
+      }
+    });
+  });
+
+  it("should preserve explicit gist deletions", () => {
+    const github: GitHubService = Object.create(GitHubService.prototype);
+    const gistObject = {
+      data: {
+        files: {
+          "extensions.json": {
+            content: "old"
+          },
+          "settings.json": {
+            content: "old"
+          }
+        }
+      }
+    };
+
+    const actual = github.UpdateChangedFiles(
+      gistObject,
+      [new File("settings.json", "new", "", "settings.json")],
+      ["extensions.json"]
+    );
+
+    expect(actual.data.files).to.deep.equals({
+      "extensions.json": null,
+      "settings.json": {
+        content: "new"
+      }
+    });
+  });
+});