The padukas were the initiative of a couple of devotees from Bombay. During their visit to Shirdi they became friendly with two local devotees, G. K. Dixit (not to be confused with H. S. "Kakasaheb" Dixit) and Sagun Meru Naik. As they were sitting talking one day, they all felt it would be good if there were some kind of memorial to Baba's advent in Shirdi and his stay under the neem tree. They first thought of laying some padukas made of rough stone. Then one of them suggested that if he put the proposal to his employer, Dr Ramrao Kothare (who had accompanied them to Shirdi), he would probably be willing to sponsor something more elegant. Dr Kothare gladly came back to Shirdi from Bombay, drew up a plan for the padukas and showed it to Upasani Baba. Sri Upasani made some improvements adding a conch, lotus, and Mahavishnu wheel, and suggested that two of his Sanskrit slokas extolling the tree's greatness and Baba's powers be inscribed on the padukas' pedestal. These slokas constitute part of Sri Sainatha Mahima Stotram, which is sung twice a day in Shirdi as part of the noon and evening aratis. They translate as follows:

I bow to Lord Sainath, who by his constant stay at the foot of the neem tree - which although bitter and unpleasant, was yet oozing nectar - made it better than the wish-fulfilling tree.

I bow to Lord Sainath, who always takes delight in resting under the neem tree and bestowing material and spiritual prosperity upon his devotees who lovingly attend on him.

The padukas were made in Bombay and sent to Shirdi. When they arrived, Baba said they should be installed on August full moon day. So on 15 August 1912 they were duly taken in ceremonious procession from Khandoba Temple to the mosque, where Baba touched them and said they were Allah's padukas and to put them at the foot of the neem tree.

Arati was already being performed every day in Sathe Wada and Dixit Wada, and with the installation of the padukas at Gurusthan, a third was started; G. K. Dixit (who had carried them on his head) was employed to officiate.

A few months after their installation the padukas were damaged by a lunatic who also destroyed some of Shirdi's temple idols. The devotees were very distressed, believing it augured ill. Baba, however, took the matter casually and told them simply to repair the crack with cement and undertake a feeding of the poor. Later, the broken padukas were replaced and the originals are said to be in the pedestal underneath.