Mohammad Mohaqiq is the founder and chairman of the People's Islamic Unity Party of Afghanistan. He had an active role in the war against the Soviet invasion of Afghanistan in 1979, fighting the Soviet Army from the northern Balkh Province. After the withdrawal of the Soviet Union from Afghanistan in 1989, Ustad Mohaqiq was appointed as the leader of the Hezb-e Wahdat for northern Afghanistan.
During the rule of the Taliban from 1996 onwards, Mohaqiq remained one of the few Mujahideen leaders who never left the country. He led United Front (Northern Alliance) Hazara resistance forces around Dar-e Suf in Samangan Province and in Yakawlang and Panjab of Bamiyan Province.
After the fall of the Taliban, he was appointed as the Vice-President and the Minister of Planning in the interim government of Afghanistan. Due to differences between him and the new Afghan President Hamid Karzai as well as Ashraf Ghani (the former Finance Minister), Mohaqiq was ousted from the cabinet by Hamid Karzai.
In 2004, Ustad Mohaqiq ran as a candidate in the Presidential Election. In some provinces like Kabul, Bamiyan, Daikundi, and even in Iran amongst the Afghan refugees, he got the majority of the votes. In the final results, he came in third position with 11.7 percent of the votes after Hamid Karzai and Yunus Qanuni.
Currently, Mohaqiq serves a Member of Parliament and the chairman of the People's Islamic Unity Party.
In 2008, in the wake of a Kuchi (Pashtun nomads) invasion into Hazara villages in Behsud and Daimirdad of Wardak Province and the indiscriminate killing of Hazaras, he went on a hunger strike protesting against the killings, incursions and the indifference of the Karzai government and the international community to these events. In July 2008, about 10,000 Hazara people came out to the streets of Kabul in support of Ustad Mohaqiq and protested against the invasion of Kuchis and discrimination against Hazaras (the third largest ethnic group in Afghanistan) by the Karzai government. Finally, Hamid Karzai issued a decree for a temporary removal of invading Kuchis from Hazara villages. After the decree and requests from various mujahideen leaders and the people to end the hunger strike, Ustad Mohaqiq ended his 8-day hunger strike.
In January 2009 an article by Ahmad Majidyar of the American Enterprise Institute included Mohaqiq on a list of fifteen possible candidates in the 2009 Afghan Presidential election. In the end, however, Mohaqiq opted to support Hamid Karzai against his main challenger Abdullah Abdullah in the election.
In 2010, Mohaqiq broke with Karzai because of Karzai's policy of appeasement towards the Taliban insurgency
In late 2011, Ahmad Zia Massoud, Haji Mohammad Mohaqiq and Abdul Rashid Dostum created the National Front of Afghanistan (also Afghanistan National Front, ANF). It is generally regarded as a reformation of the United Front (Northern Alliance) of the anti-Taliban resistance era. The National Front strongly opposes a return of the Taliban to power in Afghanistan and retains significant military capabilities. Its chairman, Ahmad Zia Massoud, is the younger brother of the former United Front leader Ahmad Shah Massoud, who was assassinated in 2001.