diff --git a/migrations/1_blank.php b/migrations/1_blank.php
new file mode 100644
index 000000000..aafb96fa8
--- /dev/null
+++ b/migrations/1_blank.php
@@ -0,0 +1,16 @@
+<?php
+
+namespace EE\Migration;
+
+/**
+ * Placeholder migration as we need migration directory in phar but we don't have any migration files.
+ *
+ * @package EE\Migration
+ */
+class Blank extends \EE\Migration\Base {
+	public function up() {
+	}
+
+	public function down() {
+	}
+}
diff --git a/php/EE/Migration/Executor.php b/php/EE/Migration/Executor.php
index bcc0ebfef..78c7e82f8 100644
--- a/php/EE/Migration/Executor.php
+++ b/php/EE/Migration/Executor.php
@@ -2,14 +2,13 @@
 
 namespace EE\Migration;
 
-use \EE;
-use \EE\Model\Migration;
-use \EE\Utils;
-use Symfony\Component\Finder\Finder;
+use EE;
+use EE\Model\Migration;
+use EE\Utils;
 
 class Executor {
 
-    const MIGRATION_PATH = EE_ROOT . '/migrations';
+    const MIGRATION_PATH = EE_ROOT . '/migrations/';
 
     /**
      * Executes all pending migrations
@@ -17,13 +16,13 @@ class Executor {
     public static function execute_migrations() {
 
         Utils\delem_log( "ee migration start" );
-        EE::log( "Migrating EasyEngine data to new version" );
+        EE::debug( "Executing migrations" );
 
         $migrations = self::get_migrations_to_execute();
 
         if( empty( $migrations ) ) {
-            EE::success( "Noting to migrate" );
-            exit( 0 );
+            EE::debug( "Nothing to migrate" );
+            return;
         }
 
         sort( $migrations );
@@ -35,7 +34,7 @@ public static function execute_migrations() {
             exit( 1 );
         }
 
-        EE::success( "Successfully migrated EasyEngine" );
+        EE::debug( "Successfully migrated EasyEngine" );
     }
 
     /**
@@ -69,7 +68,7 @@ private static function execute_migration_stack( $migrations ) {
         }
 
         try {
-            EE::log( "Migrating: $migrations[0]" );
+            EE::debug( "Migrating: $migrations[0]" );
             $migration->up();
 
             Migration::create([
@@ -78,7 +77,7 @@ private static function execute_migration_stack( $migrations ) {
             ]);
 
             $migration->status = 'complete';
-            EE::log( "Migrated: $migrations[0]" );
+            EE::debug( "Migrated: $migrations[0]" );
             $remaining_migrations = array_splice( $migrations, 1, count( $migrations ) );
             self::execute_migration_stack( $remaining_migrations );
         }
@@ -86,9 +85,9 @@ private static function execute_migration_stack( $migrations ) {
             if( $migration->status !== 'complete' ) {
                 EE::error( "Errors were encountered while processing: $migrations[0]\n" . $e->getMessage(), false );
             }
-            EE::log( "Reverting: $migrations[0]" );
+            EE::debug( "Reverting: $migrations[0]" );
             $migration->down();
-            EE::log( "Reverted: $migrations[0]" );
+            EE::debug( "Reverted: $migrations[0]" );
             throw $e;
         }
     }
@@ -103,13 +102,18 @@ private static function get_migrations_to_execute() {
     }
 
     private static function get_migrations_from_db() {
-        return Migration::all();
+        return array_column( Migration::all(), 'migration' );
     }
 
     private static function get_migrations_from_fs() {
-        // array_slice is used to remove . and .. returned by scandir()
-        $migrations = array_slice( scandir( self::MIGRATION_PATH ), 2 );
-        array_walk( $migrations, function( &$migration, $index ) {
+		$migrations = scandir( self::MIGRATION_PATH );
+
+		if( ! Utils\inside_phar() ) {
+			// array_slice is used to remove . and .. returned by scandir()
+			$migrations = array_slice( $migrations, 2 );
+		}
+
+		array_walk( $migrations, function( &$migration, $index ) {
             $migration = rtrim( $migration, '.php' );
         });
         return $migrations;
diff --git a/php/EE/Model/Option.php b/php/EE/Model/Option.php
new file mode 100644
index 000000000..f026b0a87
--- /dev/null
+++ b/php/EE/Model/Option.php
@@ -0,0 +1,53 @@
+<?php
+
+namespace EE\Model;
+
+/**
+ * Option model class.
+ */
+class Option extends Base {
+
+	protected static $table = 'options';
+
+	protected static $primary_key = 'key';
+
+	/**
+	 * Sets a key on options table
+	 *
+	 * @param string $key   Key of option
+	 * @param string $value Value of option
+	 *
+	 * @throws \Exception
+	 * @return bool Key set or not
+	 */
+	public function set( string $key, string $value ) {
+		$existing_key = static::find( $key );
+
+		if ( empty( $existing_key ) ) {
+			return static::create(
+				[
+					'key'   => $key,
+					'value' => $value,
+				]
+			);
+		}
+
+		$existing_key->value = $value;
+
+		return $existing_key->save();
+	}
+
+	/**
+	 * Gets a key from options table
+	 *
+	 * @param string $key Key of option
+	 *
+	 * @throws \Exception
+	 * @return bool|Option
+	 */
+	public function get( string $key ) {
+		$option = static::find( $key );
+
+		return false === $option ? false : $option->value;
+	}
+}
diff --git a/php/EE/Runner.php b/php/EE/Runner.php
index 248f042f5..4d381c2c5 100644
--- a/php/EE/Runner.php
+++ b/php/EE/Runner.php
@@ -2,13 +2,15 @@
 
 namespace EE;
 
+use Composer\Semver\Comparator;
 use EE;
-use EE\Utils;
 use EE\Dispatcher;
 use EE\Dispatcher\CompositeCommand;
-use Mustangostang\Spyc;
+use EE\Model\Option;
+use EE\Utils;
 use Monolog\Logger;
-use EE\Model\Site;
+use Mustangostang\Spyc;
+
 /**
  * Performs the execution of a command.
  *
@@ -59,6 +61,17 @@ private function init_ee() {
 		define( 'WEBROOT', \EE\Utils\trailingslashit( $this->config['sites_path'] ) );
 		define( 'DB', EE_CONF_ROOT.'/ee.sqlite' );
 		define( 'LOCALHOST_IP', '127.0.0.1' );
+
+		$this->maybe_trigger_migration();
+	}
+
+	/**
+	 * Function to run migrations required to upgrade to the newer version. Will always be invoked from the newer phar downloaded inside the /tmp folder
+	 */
+	private function migrate() {
+		$rsp = new \EE\RevertableStepProcessor();
+		$rsp->add_step( 'ee-migrations', 'EE\Migration\Executor::execute_migrations' );
+		return $rsp->execute();
 	}
 
 	/**
@@ -778,6 +791,33 @@ private function auto_check_update() {
 		exit;
 	}
 
+	/**
+	 * Triggers migration if current phar version > version in ee_option table
+	 */
+	private function maybe_trigger_migration() {
+		$db_version      = Option::get( 'version' );
+		$current_version = preg_replace( '/-nightly.*$/', '', EE_VERSION );
+
+		if ( ! $db_version ) {
+			$this->trigger_migration( $current_version );
+			return;
+		}
+
+		if ( Comparator::lessThan( $current_version, $db_version ) ) {
+			EE::error( 'It seems you\'re not running latest version. Please download and run latest version of EasyEngine' );
+		} elseif ( Comparator::greaterThan( $current_version, $db_version ) ) {
+			EE::log( 'Executing migrations. This might take some time.' );
+			$this->trigger_migration( $current_version );
+		}
+	}
+
+	private function trigger_migration( $version ) {
+		if ( ! $this->migrate() ) {
+			EE::error( 'There was some error while migrating. Please check logs.' );
+		}
+		Option::set( 'version', $version );
+	}
+
 	/**
 	 * Get a suggestion on similar (sub)commands when the user entered an
 	 * unknown (sub)command.
diff --git a/php/class-ee-db.php b/php/class-ee-db.php
index 0533eb362..6461fb301 100644
--- a/php/class-ee-db.php
+++ b/php/class-ee-db.php
@@ -127,6 +127,12 @@ private static function create_required_tables() {
 			PRIMARY KEY (id)
 		);';
 
+		$query .= 'CREATE TABLE options (
+			key VARCHAR NOT NULL,
+			value VARCHAR NOT NULL,
+			PRIMARY KEY (key)
+		);';
+
 		try {
 			self::$pdo->exec( $query );
 		} catch ( PDOException $exception ) {
diff --git a/php/class-ee.php b/php/class-ee.php
index 472af447b..ae1353a0c 100644
--- a/php/class-ee.php
+++ b/php/class-ee.php
@@ -94,7 +94,7 @@ public static function get_cache() {
 
 		if ( ! $cache ) {
 			$home = Utils\get_home_dir();
-			$dir = getenv( 'EE_CACHE_DIR' ) ? : "$home/.ee/cache";
+			$dir = getenv( 'EE_CACHE_DIR' ) ? : '/opt/easyengine/.cache/';
 
 			// 6 months, 300mb
 			$cache = new FileCache( $dir, 15552000, 314572800 );
diff --git a/php/commands/src/CLI_Command.php b/php/commands/src/CLI_Command.php
index 815d2af1a..5254a633d 100644
--- a/php/commands/src/CLI_Command.php
+++ b/php/commands/src/CLI_Command.php
@@ -1,9 +1,9 @@
 <?php
 
-use \Composer\Semver\Comparator;
-use \Symfony\Component\Filesystem\Filesystem;
-use \EE\Utils;
-use \EE\Model\Site;
+use Composer\Semver\Comparator;
+use EE\Model\Site;
+use EE\Utils;
+use Symfony\Component\Filesystem\Filesystem;
 
 /**
  * Review current EE info, check for updates, or see defined aliases.
@@ -154,20 +154,6 @@ public function info( $_, $assoc_args ) {
 				\EE::line( $line );
 			}
 		}
-
-		if ( '/tmp' === getcwd() ) {
-			$this->migrate();
-		}
-	}
-
-	/**
-	 * Function to run migrations required to upgrade to the newer version. Will always be invoked from the newer phar downloaded inside the /tmp folder
-	 */
-	private function migrate() {
-		$rsp = new \EE\RevertableStepProcessor();
-		$rsp->add_step( 'ee-migrations', 'EE\Migration\Executor::execute_migrations' );
-		$rsp->add_step( 'site-migration', 'EE\Migration\Containers::start_container_migration' );
-		$rsp->execute();
 	}
 
 	/**
@@ -319,6 +305,9 @@ public function update( $_, $assoc_args ) {
 		} else {
 			EE::error( "md5 hash for download ({$md5_file}) is different than the release hash ({$release_hash})." );
 		}
+
+		EE::log( 'Updating EasyEngine to new version. This might take some time.' );
+
 		$php_binary = Utils\get_php_binary();
 		$process    = EE\Process::create( "{$php_binary} $temp cli info" );
 		$result     = $process->run();
diff --git a/utils/make-phar.php b/utils/make-phar.php
index 7e4ef7d91..866c46ab1 100644
--- a/utils/make-phar.php
+++ b/utils/make-phar.php
@@ -16,9 +16,9 @@
 require EE_VENDOR_DIR . '/autoload.php';
 require EE_ROOT . '/php/utils.php';
 
-use Symfony\Component\Finder\Finder;
-use EE\Utils;
 use EE\Configurator;
+use EE\Utils;
+use Symfony\Component\Finder\Finder;
 
 $configurator = new Configurator( EE_ROOT . '/utils/make-phar-spec.php' );
 
@@ -161,6 +161,7 @@ function get_composer_versions( $current_version ) {
 	->ignoreVCS(true)
 	->name('*.php')
 	->in(EE_ROOT . '/php')
+	->in(EE_ROOT . '/migrations')
 	->in(EE_VENDOR_DIR . '/mustache')
 	->in(EE_VENDOR_DIR . '/rmccue/requests')
 	->in(EE_VENDOR_DIR . '/composer')
@@ -221,6 +222,15 @@ function get_composer_versions( $current_version ) {
 	add_file( $phar, $file );
 }
 
+if( 2 === count( scandir(__DIR__ . '/../migrations') ) ) {
+	$finder = new Finder();
+	$finder->directories()->name('migrations')->in(EE_ROOT);
+
+	foreach ( $finder as $file ) {
+		add_file( $phar, $file );
+	}
+}
+
 $finder = new Finder();
 $finder
 	->files()