Authorities in New Delhi used bulldozers to destroy a number of Muslim-owned shops on Wednesday before the Supreme Court halted the demolitions.
The action comes days after communal violence shook the capital and saw dozens arrested.
For nearly an hour after the Supreme Court order, officials continued to demolish structures, including the outer entrance and stairs into a mosque, before stopping.
Shop owners searched through the rubble of their shops afterwards to collect their belongings.
Officials say the demolition drove targeted illegal buildings and not any particular religious group.
But anti-Muslim sentiment and attacks have risen lately, and critics see the demolitions as the latest attempt to harass and marginalise Muslims under India's Hindu nationalist-led government.