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 conquest 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., Volume 2

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.

Amidst the waves of exoduses, numerous Zoroastrians stayed in Persia and converted to Islam, primarily to integrate and gain full social status under the reign of the caliphates. For approximately 200 years after the collapse of the Sasanian Empire, Persia was ruled by Arab Muslims, but the impact of Arabization was ultimately not as widespread as the rest of West Asia due Persian not being an Afroastiaic language, and the Iranian Intermezzo, which marked the resurgence of both Iranian self-governance and the Persian language, albeit with an Arabic script. Nevertheless, conditions failed to improve for the community, which continued to intermittently experience persecution as a religious minority under successive Muslim dynasties, such as the Safavids and the Qajars.

Beyond India, the global Zoroastrian population is largely concentrated in Iran, the Kurdistan Region of Iraq, and North America. In modern Iran, the religion was held in particularly high esteem under the Pahlavi dynasty, which sought to assert pre-Islamic Iranian nationalism throughout the country. Since the Islamic Revolution in 1979, it remains formally recognized by the Iranian government, which has allocated one seat in the Islamic Consultative Assembly for the Iranian Zoroastrian community.

Persecution of Zoroastrians by Christians

in the Byzantine Empire While the presence of a Zoroastrian community in the Byzantine Empire is not widely known, historical records such as those by the Roman historian Priscus in 456 indicate their existence. Priscus noted that a Sassanid ambassador condemned the harassment of Zoroastrians and attempts to force them to abandon their faith and sacred fire rituals. During conflicts between the Sassanids and the Byzantines, stipulations were sometimes made that Zoroastrians should not be persecuted; however, the very existence of such conditions implies the presence of Zoroastrians within the Byzantine realm.

During Emperor Heraclius's war against the Sassanids, the Adur Gushnasp fire temple was looted, demolished, and burned, and everyone inside was killed.

According to Mary Boyce, Zoroastrians living under Christian rule in Asia Minor were noted to have undergone hardship, notably during the long conflict between the Roman Empire and Persia. Christians living in Sassanian-held territory were noted to have destroyed many fire-temples and Zoroastrian places of worship. Christian priests deliberately extinguished the sacred fire of the Zoroastrians and characterized adherents as "followers of the wicked Zardusht (Zoroaster), serving false gods and the natural elements."

Zoroastrianism in Armenia Zoroastrianism was the official religion of the Armenians prior to the adoption of Christianity. War subsequently broke out between the Sassanids and the Armenians. During the conflict, Mushegh I Mamikonian demolished Zoroastrian temples and burned Zoroastrians alive; the Sassanids, in turn, flayed Armenians and hung their skins on walls Following the execution of Mehruzhan Artsruni, a spear—heated until it turned red was driven into his head.

Persecution by Muslims

Arab conquest of Persia

Until the Arab invasion and subsequent Muslim conquest, in the mid-7th century Persia (modern-day Iran) was a politically independent state, spanning from Mesopotamia to the Hindu Kush and dominated by a Zoroastrian majority. Zoroastrianism was the official state religion of four pre-Islamic Persian empires, the last being the Sassanian empire that passed a decree solidifying this in 224 CE. The Arab invasion abruptly brought to an end the religious domination of Zoroastrianism in Persia and instituted Islam as the official religion of the state.

Yemen's Zoroastrians who had the jizya imposed on them after being conquered by Muhammad are mentioned by the Islamic historian al-Baladhuri.

After the Muslim conquest of Persia, Zoroastrians were given dhimmi status and subjected to persecutions; discrimination and harassment began in the form of regular physical violence. Those paying Jizya were subjected to insults and humiliation by the tax collectors. Zoroastrians who were captured as slaves in wars were given their freedom if they converted to Islam.

Many fire temples, with their four axial arch openings, were usually turned into mosques simply by setting a mihrab (prayer niche) on the place of the arch nearest to qibla (the direction of Mecca). Zoroastrian temples converted into mosques in such a manner could be found in Bukhara, as well as in and near Istakhr and other Persian cities. Urban areas where Arab governors made their quarters were most vulnerable to such religious persecution, great fire temples were turned into mosques, and the citizens were forced to conform or flee. Many libraries were burnt and much cultural heritage was lost.

Gradually there were increased number of laws regulating Zoroastrian behavior, limiting their ability to participate in society, and making their life difficult in the hope that they would convert to Islam. Over time, persecution of Zoroastrians became more common and widespread, and the number of believers decreased significantly. Many converted, some superficially, to escape the systematic abuse and discrimination by the law of the land. According to Thomas Walker Arnold, Muslim missionaries did not encounter difficulty in explaining Islamic tenets to Zoroastrians, as there were many similarities between the faiths. According to Arnold, for the Persian, he would meet Ahura Mazda and Ahriman under the names of Allah and Iblis.

Once a Zoroastrian family converted to Islam, the children had to go to a madrasa to learn Arabic along with the teachings of the Quran, and these children lost their Zoroastrian identity. These factors continued to contribute to increasing rates of conversion from Zoroastrianism to Islam. A Persian scholar commented, "Why so many had to die or suffer? Because one side was determined to impose his religion upon the other who could not understand."

In the mid-7th century CE, Persia succumbed to the invading Arabs. With the death of Yazdegerd III, who was slain in 651 after being defeated in battle, the Sassanid line came to an end and the Zoroastrian faith was replaced by Islam as the national religion of Persia.

In the following centuries, Zoroastrians faced much religious discrimination and persecution, harassments, as well as being identified as najis (polluted) and impure to Muslims, making them unfit to live alongside Muslims, and therefore forcing them to evacuate from cities and face major sanctions in all spheres of life. Zoroastrians have been subject to public humiliation through dress regulations, to being labeled as najis and to exclusion in the fields of society, education and work.

Rashidun Caliphate

Under the first four (the 'Rashidun') caliphs, Persia remained predominantly Zoroastrian. Zoroastrians were given the status of 'People of the Book' or by the Arabs, although some practices contrary to Islam were prohibited. Many libraries were burnt and much cultural heritage was lost.

Umayyad Caliphate The Rashidun were followed by the Umayyads, who ruled from Syria. The persecution increased in the 8th century. The tax was imposed upon Zoroastrians, and the official language of Persia became Arabic instead of the local Persian. In 741, the Umayyads officially decreed that non-Muslims be excluded from governmental positions.

The Iranian Muslims at this time started a new tradition, which made Islam appear as a partly Iranian religion. They pointed out that an Iranian, Salman the Persian, had a great influence on the prophet Muhammad. They also pointed out the legend that Husayn, the son of Ali the fourth caliph, had married a Sassanian princess named Shahrbanu (), whose son, Ali al-Sajjad, later became the fourth Shi'a Imam. The Iranian Muslims thus believed that the Shia imams descended from Sasanian royalty. These two beliefs made it easier for Zoroastrians to convert. An instance of religious oppression is recorded when an Arab governor appointed a commissioner to supervise the destruction of shrines throughout Iran, regardless of treaty obligations. The Umayyad caliph Sulayman ibn Abd al-Malik was quoted saying, "milk the Persians and once their milk dries, suck their blood".

The Umayyad general Yazid ibn al-Muhallad was appointed the head of a great army to lead the Mazandaran expedition. On the way to Mazandaran, the general ordered captives to be hanged at the two sides of the road so that the victorious Arab army could pass through. The attack on Tabarestan (present-day Mazandaran) failed, but he established his control in Gorgan. By the orders of Yazid, so many Persians were beheaded in Gorgan that their blood mixed with water would energize the millstone to produce as much as one day meal for him, as he had vowed. The extent of his brutality represented itself by running watermills by people's blood for three days and he fed his army with the bread made from that very bloody flour. But Tabarestan remained unconquered until the majority of Zoroastrians migrated towards India and the rest converted to Islam gradually.