He is considered to have pioneered archaeological excavation techniques in India, with several significant discoveries from the prehistoric period to his credit.

He wrote an essay, "Caitya caves in the Bombay Presidency", which earned the Bhagwan Lal Indraji prize.

Wheeler, who was excavating at the site of Maiden Castle, Dorset and had perfected his field techniques (begun in 1921), was a significant influence.

I learnt here, not only what was stratigraphical digging and drawing a section and three-dimensional recording of finds [...] but was also made aware of the necessity of minute-to-minute supervision of the trench under one's charge for [...] at any moment the layer might change and [which should] be noted as early as possible" (pp. 26–27).

After returning to India, Sankalia joined Deccan College in 1939 as a professor of proto- and ancient Indian history and began systematic surveys of the monuments in and around Pune with his students.

[12] At the request of Archaeological Survey of India director general K. N. Dikshit, Sankalia undertook explorations in Gujarat to test Bruce Foote's hypothesis of a hiatus between the Lower Palaeolithic and Neolithic phases;[13] this made him into a prehistorian.

[16][17] These findings were also observed in a stratigraphical deposit at Gangapur (Gangawadi), near Nasik, where flakes, cleavers and hand axes[18] were discovered.

Sankalia's explorations in the Pravara River valley (at Nevasa) yielded palaeolithic industries and animal fossils.

[21] Sankalia's success at Nasik–Jorwe inspired him to excavate the site at Maheshwar (the Mahishmati of the Haihayas, as described in the Puranas) to prove the tradition's historicity.

[22] The horizontal excavation at Navdatoli was made in 1957–59 to reveal the settlement pattern, reconstruct the socioeconomic life of the chalcolithic people, and corroborate Sankalia's Aryan hypothesis.

[23] Sankalia's excavation at Nevasa, intended to prove (or disprove) the legend of its association with Jnaneshvara, revealed human occupation from the Lower Palaeolithic era to the Muslim-Maratha period.

[24] Sankalia went to Kashmir to study its geological deposits, which had been investigated by De Terra, Paterson, and Wadia without finding early human evidence.

When Sankalia was examining a deposit he saw a worked flake with a prominent bulb of percussion, establishing the existence of early humans in Kashmir.

The former site was found to be highly disturbed and the deposits overlying the Chalcolithic layers were too thick to be thoroughly removed, and the plan was abandoned.