diff --git a/app/config/import.js b/app/config/import.js
index bfd2e81e..c779d72c 100644
--- a/app/config/import.js
+++ b/app/config/import.js
@@ -1,4 +1,4 @@
-const {moveSync, copySync, existsSync, writeFileSync, readFileSync} = require('fs-extra');
+const {moveSync, copySync, existsSync, writeFileSync, readFileSync, lstatSync} = require('fs-extra');
 const {sync: mkdirpSync} = require('mkdirp');
 const {defaultCfg, cfgPath, legacyCfgPath, plugs, defaultPlatformKeyPath} = require('./paths');
 const {_init, _extractDefault} = require('./init');
@@ -37,41 +37,58 @@ const saveAsBackup = src => {
   throw new Error('Failed to create backup for config file. Too many backups');
 };
 
-const migrate = (old, _new, oldBackupPath) => {
-  if (old === _new) {
+// Migrate Hyper2 config to Hyper3 but only if the user hasn't manually
+// touched the new config and if the old config is not a symlink
+const migrateHyper2Config = () => {
+  if (cfgPath === legacyCfgPath) {
+    // No need to migrate
     return;
   }
-  if (existsSync(old)) {
-    //eslint-disable-next-line no-console
-    console.log('Found legacy config. Migrating ', old, '->', _new);
-    if (existsSync(_new)) {
-      saveAsBackup(_new);
-    }
-    copySync(old, _new);
-    saveAsBackup(oldBackupPath || old);
-    return true;
+  if (!existsSync(legacyCfgPath)) {
+    // Already migrated or user never used Hyper 2
+    return;
   }
-  return false;
+  const existsNew = existsSync(cfgPath);
+  if (lstatSync(legacyCfgPath).isSymbolicLink() || (existsNew && lstatSync(cfgPath).isSymbolicLink())) {
+    // One of the files is a symlink, there could be a number of complications
+    // in this case so let's avoid those and not do automatic migration
+    return;
+  }
+
+  const hasNewConfigBeenTouched = existsNew && readFileSync(cfgPath, 'utf8') !== readFileSync(defaultCfg, 'utf8');
+  if (hasNewConfigBeenTouched) {
+    // Assume the user has migrated manually but rename old config to .backup so
+    // we don't keep trying to migrate on every launch
+    const backupPath = saveAsBackup(legacyCfgPath);
+    notify(
+      'Hyper 3',
+      `Settings location has changed to ${cfgPath}.\nWe've backed up your old Hyper config to ${backupPath}`
+    );
+    return;
+  }
+
+  // Migrate
+  copySync(legacyCfgPath, cfgPath);
+  saveAsBackup(legacyCfgPath);
+
+  notify(
+    'Hyper 3',
+    `Settings location has changed to ${cfgPath}.\nWe've automatically migrated your existing config!\nPlease restart Hyper now`
+  );
 };
 
 const _importConf = function() {
   // init plugin directories if not present
   mkdirpSync(plugs.base);
-
-  // Migrate Hyper2 config to Hyper3
-  const migratedConfig = migrate(legacyCfgPath, cfgPath);
-  const migratedPlugins = migrate(plugs.legacyLocal, plugs.local, plugs.legacyBase);
-  if (migratedConfig || migratedPlugins) {
-    notify(
-      'Hyper 3',
-      `Settings location has changed to ${cfgPath}.\nWe've automatically migrated your existing config!\nPlease restart hyper`
-    );
-  }
-
-  // Run this after the migration so that we don't generate a ".backup" file for
-  // an empty local/ directory
   mkdirpSync(plugs.local);
 
+  try {
+    migrateHyper2Config();
+  } catch (err) {
+    //eslint-disable-next-line no-console
+    console.error(err);
+  }
+
   try {
     const defaultCfgRaw = readFileSync(defaultCfg, 'utf8');
     const _defaultCfg = _extractDefault(defaultCfgRaw);