Inside the tomb complex, there are the tombs of the founders of Mataram, namely Ki Ageng Pamanahan, Panembahan Senapati, and Sinuhun Seda Krapyak (Prabu Hanyakrawati) along with their families and other Mataram figures, such as Nyai Ageng Nis, Panembahan Jayaprana, Nyai Ageng Pati, Ki Ageng Juru Martani, Nyai Ageng Mataram, Kanjeng Pangeran Gagak Bening, Queen Kalinyamat, Kanjeng Ratu Retno Dumilah, and Ki Mangir Wonabaya. All the tombs of the main figures are in a large building. However, the last figure mentioned, namely Ki Mangir Wanabaya, half of his body is inside and half outside the tomb. On top of Panembahan Senapati's tomb, there is also a block of Kyai Tunggul Wulung, the vehicle of the Panembahan to meet the ruler of the South Coast.

The Old Mosque of Kota Gede was originally a prayer room (langgar) built by Sultan Agung Hanyakrakusuma. The langgar was a simple prayer room made of wood. During the reign of Paku Buwana X, the wealthy king of Kasunanan Surakarta, renovated the langgar into a magnificent mosque made of iron. The pulpit used by the preacher to deliver sermons in the mosque was a tribute from the Duke of Palembang when Sultan Agung ruled in Pleret. In addition to the pulpit, inside the mosque, precisely on the terrace of the Old Mosque of Kota Gede, there is a very old bedug, a gift from Nyai Pringgit who came from Dondong Village, Kulon Progo. For her services, Nyai Pringgit's descendants were given the right to occupy an area around the mosque which was named after her ancestor, Dondongan. In the front yard of the mosque, there is also a three meter high inscription indicating the figure behind the renovation of the mosque, namely Susuhunan Paku Buwana

Apart from the tomb and mosque, in this complex there is also Sendang Saliran. The spring is divided into two, namely the putri (female) spring and the Kangkung (male) spring. This spring is fed by water that flows right under the tomb and enters through the channel hole under the spring. Catfish type fish, live in this medium. It is said that Sendang Saliran was made by Ki Ageng Pakarahan and his son, Danang Sutawijaya. According to the story, once a turtle lived and was kept in a spring. The turtle, named Kyai Duda Rejah, lived for 100 years before his death in 1987 and was buried near the Kangkung spring.