After spending one season at Tractor, he signed a two years contract with Esteghlal on 29 May 2012. He named former Saipa head coach Majid Saleh as his assistant. Esteghlal also bought many stars like Amir Hossein Sadeghi, Rodrigo Tosi and Siavash Akbarpour from Tractor, Amin Manouchehri from Saipa, Fabio Januario from Sepahan, Javad Nekounam from Osasuna and Liam Reddy from Sydney FC. They also kept their players except Andranik Teymourian who was sold to Al-Kharitiyath and Goran Jerković to Buriram United. His side started the league disappointing in the early weeks but soon obtain leaders after a 1–0 away win over Sepahan but lose the winter championship to Sepahan at the final match of the first half. They also bought Hassan Ashjari, Farzad Hatami, Vicente Arze and Iman Mousavi in the January transfers window and Farhad Majidi returned to the first team after one season. They also released Ferydoon Zandi, Amin Manouchehri, Milad Meydavoudi, Rodrigo Tosi and Liam Reddy. They began the second half successfully and not lost until last match against Damash. Esteghlal also began season's Hazfi Cup with a 4–0 win at Saipa. On 5 May 2013, his side celebrated their 8th Iran Pro League title, 3rd under Ghalenoei with a 1–0 win over Foolad with goal from Javad Nekounam. His side also reaches to the Quarter-finals of the Champions League after ending group match in the first rank over Al-Hilal and also Al-Shabab in the Round of 16.