Fire temple in the context of "Yazd"

The persecution of Zoroastrians is a significant aspect of the later part of the community's history. It is speculated that religious strife existed between Zoroastrians and early Christians, particularly within the context of the Roman–Persian Wars, though the extent of this phenomenon remains unclear. While it was a widespread religion in West Asia for over a millennium, Zoroastrianism began to decline drastically in the aftermath of the Muslim conquest of Persia. The annexation of the Sasanian Empire by the Rashidun Caliphate marked a monumental shift for the former's Zoroastrian-majority society, which was eventually subsumed by the ensuing process of Islamization. During this period, discrimination and harassment against Zoroastrians typically took place in the form of forced conversions and sparse violence. Early Muslims who arrived in the region are recorded to have destroyed Zoroastrian temples or repurposed them as mosques. Zoroastrian practices gradually became circumscribed under Islamic law, which included the levying of the jizya, a tax on non-Muslims.

Early Muslim behaviour with Zoroastrians may have been motivated in part by the fact that they are not explicitly classified as "People of the Book" in the Quran. Although some interpretations do extend this status to the community, the wider consensus among Muslim scholars is that "People of the Book" only identifies the followers of pre-Islamic Abrahamic religions—chiefly Judaism and Christianity—and consequently excludes Zoroastrianism, which is classified as an Iranian religion. Thus, the relative lack of amnesty and privileges for Zoroastrians at this time prompted a large part of the community to flee from Persia to neighbouring India, where they were granted asylum by local kings. The descendants of these Zoroastrian refugees of the early Muslim conquests are known as the Parsi people, who comprise the most prominent community of Indian Zoroastrians today.

The conversion of non-Islamic places of worship into mosques occurred during the life of Muhammad and continued during subsequent Islamic conquests and invasions and under historical Muslim rule. Hindu temples, Jain temples, churches, synagogues, and Zoroastrian fire temples have been converted into mosques.

Several such mosques in the areas of former Muslim rule have since been reconverted or have become museums, including the Parthenon in Greece and numerous mosques in Spain, such as Mosque–Cathedral of Córdoba. Conversion of non-Islamic buildings into mosques influenced distinctive regional styles of Islamic architecture.

The Story of Sanjan (also Qissa-i Sanjan or Kisse-i Sanjan) (Persian: قصه سنجان, Gujarati: કિસે સનજાન/કિસ્સા-એ-સંજાણ) is an account of the early years of Zoroastrian settlers on the Indian subcontinent that was originally written in 1599 CE by Parsi priest, Bahman Kaikobad. In the absence of alternatives, the text is generally accepted to be the only narrative of the events described therein, and many members of the Parsi community perceive the epic poem to be an accurate account of their ancestors.

The account begins in Greater Khorasan, and narrates the travel of the emigrants to Gujarat, on the west coast of present-day India. The first chapter, which is the longest, ends with the establishment of a Fire Temple at Sanjan (Gujarat), and the later dispersion of their descendants. In later chapters, the Qissa narrates the success in repelling foreign Invaders, then the failure in the same, and the subsequent flight of the Zoroastrians. The account closes with a chapter on the conveyance of the "Fire of the Warharan" to Navsari.