The graves of most of Meher Baba's men mandali and two of His favorite masts are located in a cemetery southwest of the Jhopdhi. Though He did not specify each location, during the New Life meetings, Baba first indicated who should be interred here and gave each man the option of burial or cremation.

Most of Baba’s meetings with His women mandali preceding the New Life took place in the East Room of Meher Retreat. At that time the ashram was disbanded for the most part. But Kaikobad Dastur's wife and daughters spent the rest of their lives in the Hospital Building. And after Baba dropped the body, Kaikobad lived the last seven years of his life there. The only other person to remain on the Hill after the beginning of the New Life was Mansari, who used the three original rooms of the Kitchen Building as her quarters until she died in 1997.

The cemetery for many of Baba's close women disciples was established on the Hill where they had spent so much time with Him. Beginning with Nonny's death in 1939, their graves were placed in the rows further to the west, usually containing the cremation ashes. The monument to Baba's parents contains some of their personal items; their bodies were interred in the tower of silence in Pune. The last time Baba ever visited Meherabad was on August 11, 1962, for the burial of Gulmai, His spiritual mother. The graves of some of Baba's pet dogs and peacock are beneath the banyan tree.

When Baba established His trust in 1959, He specified the order of the graves of the women mandali to each side of His tomb. In 1971, the platform and meditation cells to the east were demolished to make that area ready. In honor of Mehera's special status as Baba's dearest disciple, the other women there opted for cremation, leaving only her body to be buried as Baba's was. Indeed the most sacred place associated with Avatar Meher Baba is His Tomb-Shrine.

Meher Baba ended the Three Incredible Weeks Sahavas of September 1954 by delivering His important “Final Declaration” at Lower Meherabad. Fourteen months later, His eastern male followers enjoyed another month of Sahavas with Him. Baba’s final Sahavas program at Meherabad was to celebrate His birthday during February 1958. During all these gatherings, Meher Baba impressed upon people how fortunate they were to bow down at His future tomb in His physical presence.

“After I drop My body, the physical remains will rest here, and this hill will become an important place of pilgrimage for the whole world. You all do not realize the importance of this day. After seventy years this place will be a place of great privilege and pilgrimage. A big town will grow up here. How fortunate you are that you are hearing about the importance of this place in the physical presence of Him to whose Samadhi (Tomb) will flock one day, from all over the world, all the lovers of God, philosophers and worshippers to pay their homage!”

On January 31st 1969, Avatar Meher Baba dropped His body at Meherazad, and His body was brought to Upper Meherabad to be buried. As the coffin and tomb were being prepared, Baba's body was kept inside His cabin on the stretcher that is still there. His body was then placed on the lid of the coffin and lowered into the crypt. It was kept surrounded by flowers, and according to hints given by Him, His body was uninterred for seven days so that His lovers from around the world might have one last chance to see His physical form. There was no sign of decomposition when the box of the coffin was placed over His body and buried on February 7th.

The Italian Carrerra marble slab over Baba’s tomb was installed by Padri in late 1971.The exterior colors of the Samadhi were chosen by Mehera and Mani in the late 1980s, and a complete restoration of the original building was done in 1990. In 1991, in lieu of a stained glass work by Charlie Morton for the north window, Mani decided that his painting should be installed there instead. Today the Samadhi is the most sacred place at Meherabad and the heart of the legacy that the Trust care-takes for humanity.