In 1386, Timur captured
Tabriz, the capital of the
Jalairid Sultanate. Muhammad Sultan, then only ten years old, was appointed governor of the city. Five years later, he accompanied his grandfather in his invasion of the territory of
Tokhtamysh, Khan of the Golden Horde. Initially part of the scouting parties which preceded the army, Timur later gave him command of the army centre, a position he held during the ensuing
Battle of the Kondurcha River in June 1391. In 1393, he took part in the campaign against the
Muzaffarids of
Fars. He, along with his younger half-brother
Pir Muhammad, were sent through
Kurdistan, capturing various provinces, with orders to later re-join the main army. Timur himself pursued the Muzaffarid king,
Shah Mansur. The armies of the two rulers met outside the city of
Shiraz; Timur entrusted his left flank to Muhammad Sultan, the right to Pir Muhammad whilst the centre was given to their uncle
Shah Rukh. The battle ultimately resulted in a Timurid victory, with Shah Mansur being killed by Timur's soldiers and his lands subsequently being incorporated into the empire. Muhammad Sultan once more joined Timur in his war against Tokhtamysh in 1395, accompanying the emperor in a second invasion of the
Golden Horde. He led the right wing of the army during the
Battle of the Terek River and inflicted heavy damage on the Khan's left flank, forcing it into retreat, with Tokhtamysh himself fleeing soon after. The following year, he was dispatched to the kingdom of
Hormuz on the
Persian Gulf. After capturing various provincial forts, the prince compelled the ruler, Muhammad Shah, to submit. In 1397, he was named governor of the eastern province of
Ferghana. With the idea of an eventual campaign against
China in mind, Timur ordered his grandson to consolidate bases in the region, as well as develop soil cultivation along the route. Muhammad Sultan was given an army of forty thousand and had a fort built in the region of Ashapara, followed by another further east by the
Issyk-Kul. The prince intended to use these as a frontier line for operations against the neighbouring kingdom of
Moghulistan in 1399. However, this plan was forestalled when his cousin,
Iskandar Mirza, drew on Muhammad Sultan's detachments at Ashpara to launch a raid into Chinese
Turkestan. This arbitrary action resulted in a grudge between the two princes. Less than a year later, after Iskandar had been transferred to Ferghana while Muhammad Sultan himself was named custodian of
Samarqand, the latter had his cousin captured and detained within the city. Iskandar's
atabeg and twenty-six of his nobles were executed. Reports of Timur's reaction to the feud are contradictory; one account states that Timur blamed Muhammad Sultan for the dispute and upheld Iskandar, ordering restitution for his nobles. Another says that Timur sided with the former and had Iskandar's
feet whipped as punishment. The prince supposedly pushed Timur to pursue his campaign against the
Delhi Sultanate in 1398. The
Malfuzat-i Timuri, an alleged autobiography of the emperor, ascribes the following speech to Muhammad Sultan: ==As Timur's heir==