It was the tradition of Moghul princes to develop sites for recreation and pleasure during their lifetime, and choose one of these as a last resting-place. The site continued to be of significance to Babur’s successors, Jehangir and his step-mother, Empress Ruqaiya Sultan Begum (Babur's granddaughter) made a pilgrimage to the site in 1607 AD (1016 AH) when he ordered that all gardens in Kabul be surrounded by walls, that a prayer platform be laid in front of Babur’s grave, and an inscribed headstone placed at its head. During the visit of the Mughal Emperor Shah Jahan in 1638 (1047 AH) a marble screen was erected around tomb of his foster-mother, Ruqaiya Sultan Begum, and a mosque built on the terrace below. There are accounts from the time of the visit to the site of Shah Jahan in 1638 (1047AH) of a stone water-channel that ran between an avenue of trees from the terrace below the mosque, with pools at certain intervals.
The original construction date of the gardens is unknown. When Babur captured Kabul in 1504 from the Arguns he re-developed the site and used it as a guest house for special occasions, especially during the summer seasons. Since Babur had such a high rank, he would have been buried in a site that befitted him. The garden where it is believed Babur requested to be buried in is known as Bagh-e Babur. Mughul rulers saw this site as significant and aided in further development of the site and other tombs in Kabul. In an article written by the Aga Khan Historic Cities Programme, describes the marble screen built around tombs by Mughal Emperor Shah Jahan in 1638 with the following inscription:
"only this mosque of beauty, this temple of nobility, constructed for the prayer of saints and the epiphany of cherubs, was fit to stand in so venerable a sanctuary as this highway of archangels, this theatre of heaven, the light garden of the godforgiven angel king whose rest is in the garden of heaven, Zahiruddin Muhammad Babur the Conqueror."
Although the additions of the screens by Shah Jahan contained references to Babur, Salome Zajadacz-Hastenrath, in her article "A Note on Babur's Lost Funerary and Enclosure at Kabul" suggests that Shah Jahan's work transformed Bagh-e Babur into a graveyard. She states that a "mosque was built on the thirteenth terrace, the terrace nearest to Mecca; the next, the fourteenth terrace, was to contain the funerary enclosure of Babur's tomb and the tombs of some of his male relatives." This transformation towards a proper graveyard, with an enclosure around Babur's tomb, points towards the importance of Babur. By enclosing Babur's tomb, Shah Jahan separates the tomb of the Emperor from others.
The only hint of the design lies in an 1832 sketch and short description by Charles Masson, a British soldier, which was published in 1842, the year the tomb was destroyed by an earthquake. One description of the tomb praised it, "although obviously-in a poor state of preservation, reveals fine workmanship in stone carving: high walls with lavish jali-work and relief decoration." Mason described the tomb as being "accompanied by many monuments of similar nature, commemorative of his relatives, and they are surrounded by an enclosure of white marble, curiously and elegantly carved... No person superintends them, and great liberty has been taken with the stones employed in the enclosing walls." Mason's sketch and Mason's description gives us the only modern view of how extravagant the tomb was.