The arrival of Shamsuddin Hasan at Kohistan marked with the outbreak of new conflicts between the Ismailis and their Sistan neighbours. Yaminuddin Bahram Shah bin Taj al-Din Harb (610-618/1213-1221), the local Nasrid chief of Sistan, had previously waged two wars against Alamut during the time of Imam Jalaluddin Hasan; and his nephew had sold the fortress of Shahanshah near the town of Nih to Alamut. Yaminuddin demanded from the Ismailis of Kohistan to give up the claim of the fortress, and threatened to capture it by force. Before the invasion of Yaminuddin on Kohistan, the four fidais had killed him on 5th Rabi II, 618/May 29, 1221 at Zarang.
It was followed immediately by the succession issue in Sistan among the sons of Yaminuddin. The Ismailis of Kohistan supported Ruknuddin against his younger brother Nusratuddin, whom the notables placed on the throne. Like his father, Nusratuddin continued his claim on the fortress of Shahanshah. Soon afterwards, Ruknuddin gained the throne of Sistan with the help of the Ismailis in 619/1222. In the meantime, the Mongols invaded Sistan without staying there, and Ruknuddin had also been killed by his slave. The notables of Sistan put on the throne Shihabuddin bin Harb and his brother Ali, to the dissatisfaction of the Ismailis, who again had their own candidate, Uthman Shah bin Nasiruddin Uthman. They acquired support from Khwarazmian commander, called Tajuddin Yinaltagin, who was then stationed at Kirman, for the rights of Uthman. Yinaltagin arrived in 622/1225 at Sistan with his troops, and defeated the forces of Sistan. Instead of placing Uthman on the throne, Yinaltagin retained this power with him for almost a decade.
Thus, Shamsuddin, the Ismaili governor of Kohistan commanded his forces in a battle against Yinaltagin, and inflicted a defeat to him in 623/1226. It was after this battle against Yinaltagin, who deputed Minhaj Siraj Juzjani as his envoy to conduct diplomatic negotiations with the Ismailis of Kohistan. Minhaj Siraj concluded a truce with Shamsuddin at Nih on behalf of Yinaltagin, and as a result, the Ismailis pursued an independent policy in its local affairs, and developed important trade route with other regions, which were the source of acceleration of their economical conditions. When Minhaj Siraj returned to Sistan after negotiations, Yinaltagin forced him to go once again to Kohistan to declare a war against the Ismailis, but he did not consent to set out on a second journey, as he had determined upon undertaking a journey into India. This refusal did not meet with the approval of Yinaltagin and he commanded to detain him for 43 days in the fort of Safhad of Sistan and prohibited his going beyond the walls.
In the meantime, Alamut gave refuge to Ozbeg's son, Malik Khamush, and to Jalaluddin's brother Ghiasuddin, who were dismissed from their posts by the Khwarazmshah in 625/1228. The Ismailis helped Ghiasuddin despite the Khawarazmian blockade of Rudhbar, but he was there murdered.
In 625/1228, while the Ismaili envoy Badruddin was travelling east across the Oxus to Mongol court, Jalaluddin Khwarazmshah ordered at once to stop all the caravans in that direction, pretending that a Mongol envoy was on his way to Syria in the company of some Ismailis. In compliance, his vizir Sharaf al-Mulk put to death in Azerbaijan a westward Syrian Ismaili caravan of seventy merchants. Hence, Alamut sent an emissary to the Khwarazmshah, demanding successfully retrieval of the goods taken from the murdered Syrian Ismailis. In the meantime, Ghiasuddin took flight from Alamut which had enraged Jalaluddin Khwarazmshah.