The first Muslim Empire of India, the Sultanate of Delhi, was established in 1210 CE by Turkic tribes that invaded the subcontinent from Afghanistan. Many temples were looted and destroyed. Infamous cases include the destruction of the Somnath.
Muhammad Ghori committed genocide against Hindus at Koi (modern Aligarh), Kalinjar and Varanasi, according to Hasan Nizami's Taj-ul-Maasir, 20,000 Hindu prisoners were slaughtered and their heads offered to crows.