The first Siddis are thought to have arrived in India in 628 AD at the Bharuch port. Several others followed with the first Arab Islamic invasions of the subcontinent in 712 AD. The latter group are believed to have been soldiers with Muhammad bin Qasim's Arab army, and were called "Zanjis".

Most Siddis, however, are believed to be the descendants of slaves, sailors, servants and merchants from East Africa who arrived and became resident in the subcontinent during the 1200-1900 AD period. A large influx of Siddis to the region occurred in the 17th century when Portuguese slave traders sold a number of them to local princes.

In Western India (the modern Indian states of Gujarat and Maharashtra), the Siddi gained a reputation for physical strength and loyalty, and were sought out as mercenaries by local rulers, and as domestic servants and farm labor. Some Siddis escaped slavery to establish communities in forested areas, and some even established small Siddi principalities on Janjira Island and at Jaffrabad as early as the twelfth century. A former alternative name of Janjira was Habshan (i.e., land of the Habshis). In the Delhi Sultanate period prior to the rise of the Mughals in India, Jamal-ud-Din Yaqut was a prominent Siddi slave-turned-nobleman who was a close confidant of Razia Sultana (1205–1240 CE). Although this is disputed, he may also have been her lover.

As a power centre, Siddis were sometimes allied with the Mughal Empire in its power-struggle with the Maratha Confederacy. However, Malik Ambar, a prominent Siddi figure in Indian history at large, is sometimes regarded as the "military guru of the Marathas", and was deeply allied with them. He established the town of Khirki which later became the modern city of Aurangabad, and helped establish the Marathas as a major force in the Deccan. Later, the Marathas adapted Siddi guerrilla warfare tactics to grow their power and ultimately demolish the Mughal empire. Some accounts describe the Mughal emperor Jahangir as obsessed by Ambar due to the Mughal empire's consistent failures in crushing him and his Maratha cavalry, describing him derogatorily as "the black faced" and "the ill-starred" in the royal chronicles and even having a painting commissioned that showed Jahangir killing Ambar, a fantasy which was never realised in reality.

Most Siddis are descended from Bantu peoples from Southeast Africa that were brought by the Portuguese. While most of these migrants became Muslim and a small minority became Christian, very few became Hindu since they could not find themselves a position in the traditional Hindu caste hierarchy.

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