Mohammad Shah dismissed and executed his tactful premier, Abol-Qasem Qa'em-Maqam, and appointed his favourite, Haji Mirza Aqasi, as the grand vizier.

Mohammad was devoted to both Aqasi and his teachings on Sufism; he became a willing sustainer of Sufis, and sought spiritual guidance in mystical rituals instead of the marji'i taqlīd (Shiite clerics).

Mohammad enlarged the Qajar bureaucracy, and filled governmental positions with Aqasi's Sufi friends and companions, thus establishing a corrupt administration that saw its peak during his son's reign.

[3] Though his realm never reached the far east of Greater Khorasan, he was recognised as the Shahanshah by Ahmad Shah Durrani, who proclaimed his allegiance in a public khutba.

During the reign of Fath-Ali Shah, tensions in Iranian-Russian relations escalated and turned into two full scale wars which saw the defeat of Iran in several stages.

In the resulting battle, Amir Khan was killed and Mohammad was severely defeated and forced to retreat;[15] he, however, was praised for his efforts during the war and was nicknamed a Gazi (warrior of Islam).

In one of his missions, Mohammad released nearly 20,000 Iranians held captive by Central Asian Sunni tribes; in honor of this victory, he named his newborn child "Naser al-Din" (defender of the faith).

[20] Abbas Mirza spent two years in Khorasan suppressing rebel khans; Khiva and Herat supported these revolts and promised aid but Mohammad's victories discouraged them.

It was agreed that Kamran would accept the sovereignty of Iran, pay 15,000 tomans in gold and fifty Kashmir shawls, and release the Iranian prisoners who had been captured during the war.

[23] At Nowruz (Iranian New Year, which is held at the March equinox) of 1834, Mohammad Mirza was appointed the crown prince and took the governorship of Azarbaijan—the office of his father—and left Tehran for Tabriz.

[30] In October 1834, Fath-Ali Shah, with the intention of collecting 200,000 tomans of tax arrears from Hossein Ali Mirza, went to Fars but died en route at Isfahan.

[32] In early November, John Campbell and Comte Ivan Simonich, the British and Russian envoys, arrived in Tabriz to proclaim their support for Mohammad Mirza.

[31] Hossein Ali was imprisoned in Ardabil and soon died of cholera; with his defeat, the other rebel princes surrendered their claims and recognized Mohammad as the king of Iran.

[45] When Mohammad Shah ascended the throne, on the advice of Qa'em Maqam, he had appointed Agha Khan as the governor of Kerman, a rebellious state that was governed by Shoja al-Saltanah, a brother of Hossein Ali Mirza.

[47] This alarmed Kamran Shah and prompted him to attempt to gather the neighboring tribes such as the Jamshidi, Tumani and Hazara in Herat to fight Mohammad in the event of a military campaign.

Thus, under the leadership of Sher Mohammad and Kamran Shah's son Nader Mirza, ten to twelve thousand horsemen had assembled around Qala-e Naw and threatened to attack Iran's borders.

[60] Eventually, Asaf al-Dowleh and his men marched through the mountains to Bala Murghab and from there to Maymana, where he defeated another host of the Afghan army under the command of Sher Mohammad Khan.

[61] On 23 November, Mohammad Shah with a part of his army reached the outskirts of Herat, where they faced fierce resistance from the defenders but eventually forced them to retreat behind the city walls.

[62] The Iranian army were divided in opinion; Aqasi wanted to wait for Russian aid[63] whereas Mirza Aqa Khan Nuri had argued for crushing the city walls.

[18] Hostilities with the Ottomans and tensions over the borderlands of the two empires had not been resolved by the treaty of Erzurum and later led to incidents during Mohammad Shah's reign that pushed him to start a war, such as the sack of Khorramshahr by Ali Reza Pasha, the governor of Baghdad, in 1837.

[79] On the Ottoman side was Enveri Sadullah Efendi, a member of the Supreme Council of Justice, whose arrogance and occasional undiplomatic language created so many problems that he was once considered to be replaced.

[83] Ownership of Zohab was a heated argument between negotiators; the town, which was insignificant in itself, had been captured by Mohamad Ali Mirza Dowlatshah, the firstborn son of Fath-Ali Shah, during the Ottoman-Persian war of 1821.

[84] Farahani suggested that Zohab be divided between the two nations, but the Iranian party later agreed to cede the town to the Ottomans who, in return, would forsake their desire to dominate the Shatt al-Arab's trade route.

Not wanting to make Mohammad Shah suspicious, the British and Russian ambassadors persuaded Mirza Mohammad-Ali Khan Shirazi, Iran's envoy to France who was in Istanbul at the time, to ratify the new articles, alternatively called the "Explanatory Note".

[15] Influenced by Aqasi, he had refused to be treated by European doctors, and instead trusted the traditional treatment of a fraudster, which gave him a severe paroxysm,[99] due to which Mohammad became so weak that rumours of his impending death spread throughout Tehran.

Mohammad would not accept these requests in his early years, arguing that a culprit does not deserve sympathy, but as he aged and grew weaker from gout, he ordered the complete abolition of torture.

[129] Aqasi enlarged governmental titles and promoted his kinsmen, thuz the once-rudimentary bureaucracy of Agha Mohammad Khan became filled with positions with the same duties but under different names.

[44] The threat of the Russian military bordering Azerbaijan and their navy anchoring in the port of Anzali Lagoon put Mohammad Shah in a state of paranoia at the thought of another war.

[141] After the signing of the agreement, inexpensive British goods entered Iran through the Tabriz-Trabzon trade zone and filled the country's markets, causing the bankruptcy of a number of Iranian businessmen in Tabriz.

[159] Travel writer James Baillie Fraser, who met Mohammad in 1834, described him as "the worthiest of all the numerous descendants of Fath-Ali Shah, particularly in the points of moral and private character".