It is not always clear whether the fall of Saljuks at the end of the 12th century changed the situation of religious minorities. In the west of Iran the Saljuks were in competition with the Abbasid caliphs such as al-Muqtafi, who in 1152 expelled the Saljuk officials from Baghdad, and al-Nasir who assumed full power in Iraq in 1180-1225. The Caliph al-Nasir decreed the discharge of non-Muslims from official functions. The Saljuks had already cleansed their administration of Christians and Jews a century earlier. Consequently, the fall of the Saljuks in the East must have overjoyed the non-Muslim communities. The Chinese Qara Khitais, who defeated the Saljuk Sultan Sanjar in 1141, were not Muslims and had no strong religious inclinations, and therefore did not discriminate on a religious basis. Nonetheless, the non-Muslims were not given much time to benefit from the rule of the Qara Khitai, as by 1212 they were completely evicted from Transoxania by the Muslim Khwarazmshahs, who struggled to dominate central and eastern Persia between 1156 and 1215.
While the realm of Islam seemed unshakeable, in outer Mongolia in 1206 a very capable chieftain called Gengis Khan imposed himself as the leader of the Mongols. Three of the tribes he had rallied to his cause were Nestorian, converted by missionaries from Iran a few centuries earlier. Gengis Khan relied heavily on them for the administration of his country. Juwayni tells us that he ordered the Mongols to learn the Uighur script (which emanated from the Syriac script of the Nestorians) from them, and had their legal code written down in that script. This markedly increased their influence and prestige among the Mongols. As a result, Gengis Khan and his followers held the Christians in high regard, but we know from the sources, such as Juwayni’s and Rashid al-Din’s works, that Muslims were also appreciated for their skills. When Gengis Khan’s son, Tolui, captured the town of Merv, he spared the lives of four hundred artisans, but his army and the people of the rival neighbouring town of Sarakhs were allowed to slaughter the rest of the population.The brutality and intransigence of the Mongols in battle has brought some western authors, such as Wilhelm von Rubruck, to call the Mongols savages and depict them as indifferent to religious matters. However, Bar Hebraeus, a Jacobite Christian and witness to the events of the period, admired their religious tolerance.