diff --git a/.github/manual-test b/.github/manual-test
index db2dca4..160c636 100755
--- a/.github/manual-test
+++ b/.github/manual-test
@@ -104,3 +104,38 @@ printf '\n***** SMOKE TEST 3: Test checklist *****
 
 launch_app "$tmp_dir" "$name"
 request_feedback "$tmp_dir"
+
+# ------------------------------------------------------------------------------
+
+printf '\n***** SMOKE TEST 4: Setting up test and building app... *****\n'
+tmp_dir=$(mktemp -d -t nativefier-manual-test-tray-XXXXX)
+name='nativefier-smoke-test-4'
+node ./lib/cli.js 'https://google.com/' \
+  --name "$name" \
+  --tray \
+  "$tmp_dir"
+
+printf '\n***** SMOKE TEST 4: Test checklist *****
+- Should have an app with a tray icon
+- Console: no Electron runtime deprecation warnings/error logged'
+
+launch_app "$tmp_dir" "$name"
+request_feedback "$tmp_dir"
+
+# ------------------------------------------------------------------------------
+
+printf '\n***** SMOKE TEST 5: Setting up test and building app... *****\n'
+tmp_dir=$(mktemp -d -t nativefier-manual-test-start-in-tray-XXXXX)
+name='nativefier-smoke-test-5'
+node ./lib/cli.js 'https://google.com/' \
+  --name "$name" \
+  --tray start-in-tray \
+  "$tmp_dir"
+
+printf '\n***** SMOKE TEST 5: Test checklist *****
+- Should have an app that does not show a window initially,
+  but will have a tray icon that will show the window.
+- Console: no Electron runtime deprecation warnings/error logged'
+
+launch_app "$tmp_dir" "$name"
+request_feedback "$tmp_dir"
diff --git a/app/src/components/mainWindow.ts b/app/src/components/mainWindow.ts
index 5ef08c0..c002432 100644
--- a/app/src/components/mainWindow.ts
+++ b/app/src/components/mainWindow.ts
@@ -146,7 +146,7 @@ function createContextMenu(options, window: BrowserWindow): void {
 
 export function saveAppArgs(newAppArgs: any): void {
   try {
-    fs.writeFileSync(APP_ARGS_FILE_PATH, JSON.stringify(newAppArgs));
+    fs.writeFileSync(APP_ARGS_FILE_PATH, JSON.stringify(newAppArgs, null, 2));
   } catch (err: unknown) {
     log.warn(
       `WARNING: Ignored nativefier.json rewrital (${(err as Error).message})`,
diff --git a/src/build/prepareElectronApp.ts b/src/build/prepareElectronApp.ts
index c40baf0..51df923 100644
--- a/src/build/prepareElectronApp.ts
+++ b/src/build/prepareElectronApp.ts
@@ -165,7 +165,7 @@ function changeAppPackageJsonName(
   packageJson.name = normalizedAppName;
   log.debug(`Updating ${packageJsonPath} 'name' field to ${normalizedAppName}`);
 
-  fs.writeFileSync(packageJsonPath, JSON.stringify(packageJson));
+  fs.writeFileSync(packageJsonPath, JSON.stringify(packageJson, null, 2));
 }
 
 /**
@@ -190,7 +190,7 @@ export async function prepareElectronApp(
   log.debug(`Writing app config to ${appJsonPath}`);
   await writeFileAsync(
     appJsonPath,
-    JSON.stringify(pickElectronAppArgs(options)),
+    JSON.stringify(pickElectronAppArgs(options), null, 2),
   );
 
   if (options.nativefier.bookmarksMenu) {
diff --git a/src/cli.test.ts b/src/cli.test.ts
index c4b9693..0e7c0f3 100644
--- a/src/cli.test.ts
+++ b/src/cli.test.ts
@@ -130,6 +130,7 @@ describe('initArgs + parseArgs', () => {
       isJsonString: true,
     },
     { arg: 'proxy-rules', shortArg: '', value: 'RULE: PROXY' },
+    { arg: 'tray', shortArg: '', value: 'true' },
     { arg: 'user-agent', shortArg: 'u', value: 'FIREFOX' },
     {
       arg: 'win32metadata',
@@ -220,7 +221,6 @@ describe('initArgs + parseArgs', () => {
     { arg: 'portable', shortArg: '' },
     { arg: 'show-menu-bar', shortArg: 'm' },
     { arg: 'single-instance', shortArg: '' },
-    { arg: 'tray', shortArg: '' },
     { arg: 'verbose', shortArg: '' },
     { arg: 'widevine', shortArg: '' },
   ])('test boolean arg %s', ({ arg, shortArg }) => {
@@ -303,4 +303,29 @@ describe('initArgs + parseArgs', () => {
       expect(badShortArgs[arg]).toBeNaN();
     }
   });
+
+  test.each([
+    { arg: 'tray', value: 'true' },
+    { arg: 'tray', value: 'false' },
+    { arg: 'tray', value: 'start-in-tray' },
+    { arg: 'tray', value: '' },
+    { arg: 'tray', value: undefined },
+  ])('test tray valyue %s', ({ arg, value }) => {
+    if (value !== undefined) {
+      const args = parseArgs(
+        initArgs(['https://google.com', `--${arg}`, `${value}`]),
+      ) as Record<string, number>;
+      if (value !== '') {
+        expect(args[arg]).toBe(value);
+      } else {
+        expect(args[arg]).toBe('true');
+      }
+    } else {
+      const args = parseArgs(initArgs(['https://google.com'])) as Record<
+        string,
+        number
+      >;
+      expect(args[arg]).toBe('false');
+    }
+  });
 });
diff --git a/src/cli.ts b/src/cli.ts
index a6ec98d..4f88bf0 100755
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -1,9 +1,11 @@
 #!/usr/bin/env node
 import 'source-map-support/register';
 
+import electronPackager = require('electron-packager');
 import * as log from 'loglevel';
 import * as yargs from 'yargs';
 
+import { DEFAULT_ELECTRON_VERSION } from './constants';
 import {
   checkInternet,
   getProcessEnvs,
@@ -13,11 +15,10 @@ import { supportedArchs, supportedPlatforms } from './infer/inferOs';
 import { buildNativefierApp } from './main';
 import { RawOptions } from './options/model';
 import { parseJson } from './utils/parseUtils';
-import { DEFAULT_ELECTRON_VERSION } from './constants';
-import electronPackager = require('electron-packager');
 
 export function initArgs(argv: string[]): yargs.Argv<RawOptions> {
-  const args = yargs(argv)
+  const sanitizedArgs = sanitizeArgs(argv);
+  const args = yargs(sanitizedArgs)
     .scriptName('nativefier')
     .usage(
       '$0 <targetUrl> [outputDirectory] [other options]\nor\n$0 --upgrade <pathToExistingApp> [other options]',
@@ -229,10 +230,10 @@ export function initArgs(argv: string[]): yargs.Argv<RawOptions> {
       type: 'boolean',
     })
     .option('tray', {
-      default: false,
+      default: 'false',
       description:
         "allow app to stay in system tray. If 'start-in-tray' is set as argument, don't show main window on first start",
-      type: 'boolean',
+      type: 'string',
     })
     .option('width', {
       defaultDescription: '1280',
@@ -569,18 +570,20 @@ export function parseArgs(args: yargs.Argv<RawOptions>): RawOptions {
   return parsed;
 }
 
-if (require.main === module) {
-  // Not sure if we still need this with yargs. Keeping for now.
+function sanitizeArgs(argv: string[]): string[] {
   const sanitizedArgs: string[] = [];
-  process.argv.forEach((arg) => {
+  argv.forEach((arg) => {
     if (isArgFormatInvalid(arg)) {
       throw new Error(
         `Invalid argument passed: ${arg} .\nNativefier supports short options (like "-n") and long options (like "--name"), all lowercase. Run "nativefier --help" for help.\nAborting`,
       );
     }
+    const isLastArg = sanitizedArgs.length + 1 === argv.length;
     if (sanitizedArgs.length > 0) {
       const previousArg = sanitizedArgs[sanitizedArgs.length - 1];
 
+      log.debug({ arg, previousArg, isLastArg });
+
       // Work around commander.js not supporting default argument for options
       if (
         previousArg === '--tray' &&
@@ -590,12 +593,21 @@ if (require.main === module) {
       }
     }
     sanitizedArgs.push(arg);
+
+    if (arg === '--tray' && isLastArg) {
+      // Add a true if --tray is last so it gets enabled
+      sanitizedArgs.push('true');
+    }
   });
 
+  return sanitizedArgs;
+}
+
+if (require.main === module) {
   let args: yargs.Argv<RawOptions> | undefined = undefined;
   let parsedArgs: RawOptions;
   try {
-    args = initArgs(sanitizedArgs.slice(2));
+    args = initArgs(process.argv.slice(2));
     parsedArgs = parseArgs(args);
   } catch (err: unknown) {
     if (args) {