diff --git a/cli/src/lib/generateManifests.js b/cli/src/lib/generateManifests.js
index 212766e76..6ba6db624 100644
--- a/cli/src/lib/generateManifests.js
+++ b/cli/src/lib/generateManifests.js
@@ -1,6 +1,28 @@
 const { reporter, chalk } = require('@dhis2/cli-helpers-engine')
 const fs = require('fs-extra')
 
+/**
+ * Gets the original `entrypoints` property in d2.config.js
+ * without applying defaults. Used to detect if there is actually
+ * supposed to be an app entrypoint for this... app. Temporary until
+ * the build process is redesigned to allow building plugins without
+ * apps (LIBS-479)
+ */
+const getOriginalEntrypoints = (paths) => {
+    try {
+        if (fs.existsSync(paths.config)) {
+            reporter.debug('Loading d2 config at', paths.config)
+            // NB: this import can be confounded by previous object mutations
+            const originalConfig = require(paths.config)
+            reporter.debug('loaded', originalConfig)
+            return originalConfig.entryPoints // may be undefined
+        }
+    } catch (e) {
+        reporter.error('Failed to load d2 config!')
+        reporter.error(e)
+        process.exit(1)
+    }
+}
 const parseCustomAuthorities = (authorities) => {
     if (!authorities) {
         return undefined
@@ -93,11 +115,20 @@ module.exports = (paths, config, publicUrl) => {
             },
         ],
         start_url: '.',
-        display: 'browser',
+        display: 'standalone',
         theme_color: '#ffffff',
         background_color: '#f4f6f8',
     }
 
+    const includesPlugin = Boolean(config.entryPoints.plugin)
+    // If there's a plugin, there might not be an app intended to be exposed,
+    // in which case omit the app launch path. Check the original d2.config
+    // without added defaults to see if an app is intended.
+    // If there's not a plugin, default to 'true'
+    const shouldIncludeAppLaunchPath = includesPlugin
+        ? Boolean(getOriginalEntrypoints(paths)?.app)
+        : true
+
     // Legacy manifest
     const manifestWebapp = {
         app_hub_id: config.id,
@@ -108,8 +139,8 @@ module.exports = (paths, config, publicUrl) => {
         version: config.version,
         core_app: config.coreApp,
 
-        launch_path: paths.launchPath,
-        plugin_launch_path: paths.pluginLaunchPath,
+        launch_path: shouldIncludeAppLaunchPath ? paths.launchPath : undefined,
+        plugin_launch_path: includesPlugin ? paths.pluginLaunchPath : undefined,
         default_locale: 'en',
         activities: {
             dhis: {
@@ -148,8 +179,8 @@ module.exports = (paths, config, publicUrl) => {
     const appConfig = { ...config }
     delete appConfig['entryPoints']
     appConfig.entryPoints = {
-        app: paths.launchPath,
-        plugin: config.entryPoints.plugin ? paths.pluginLaunchPath : undefined,
+        app: shouldIncludeAppLaunchPath ? paths.launchPath : undefined,
+        plugin: includesPlugin ? paths.pluginLaunchPath : undefined,
     }
     delete appConfig['pwa']
 
diff --git a/cli/src/lib/parseConfig.js b/cli/src/lib/parseConfig.js
index 9d5f7c5cf..72cf0de6f 100644
--- a/cli/src/lib/parseConfig.js
+++ b/cli/src/lib/parseConfig.js
@@ -1,6 +1,6 @@
 const { reporter, chalk } = require('@dhis2/cli-helpers-engine')
 const fs = require('fs-extra')
-const { defaultsDeep, has, isPlainObject } = require('lodash')
+const { defaultsDeep, cloneDeep, has, isPlainObject } = require('lodash')
 const parseAuthorString = require('parse-author')
 
 const requiredConfigFields = {
@@ -83,7 +83,10 @@ const parseConfig = (paths) => {
 
         if (fs.existsSync(paths.config)) {
             reporter.debug('Loading d2 config at', paths.config)
-            config = require(paths.config)
+            const importedConfig = require(paths.config)
+            // Make sure not to overwrite imported object
+            // (need to use it later in generateManifest)
+            config = cloneDeep(importedConfig)
             reporter.debug('loaded', config)
         }
         if (fs.existsSync(paths.package)) {