After being homeschooled, he arrived in Baku in 1903 to work in the oil fields. He was ordered imprisoned for one year in 1909 and temporarily refused the right to stay in Baku. Upon his release he returned to his native Tugh to continue his education and established contact with prominent scholars of neighbouring Shusha, one of the largest cultural centres of the Caucasus.
He returned to Baku in 1914 and was hired as a clerk at the Shibayev and Company oil company.
That same year he joined the Musavat Party and enrolled in an undergraduate technical school. During that period he acquired several languages in addition to those he had already known.
By the time of Azerbaijan"s independence in 1918 besides his native Azeri Malik-Yeganov was fluent in Russian, German, Persian, Armenian, and Georgian. In 1917, Javad Malik-Yeganov was elected in the Transcaucasian Sejm as a representative for the South Caucasus" Azeri community.
On 10 March 1919 he was included in the committee in charge of investigating and reporting on the economic problems of Baku"s working class.
In June 1919 he became Governor-General of Lankaran after the fall of the British-backed Provisional Military Dictatorship of Mughan and its successor, the Mughan Soviet Republic. His brief governance was marked by major social developments in Azerbaijan"s southeastern regions, including the opening of new schools, libraries and cultural clubs, as well as the encouragement for girls to receive education. He also managed to reconcile the local Azeri population with the pro-Bolshevik representatives of the local Russian community and the Armenian volunteers who fought on their side.
Malik-Yeganov remained in that position until Azerbaijan"s Sovietization on 28 April 1920.
He immediately fell under suspicion in the eyes of the Communist leaders. In the next 18 years he would be imprisoned 6 times.
In the 1920s he worked in the construction trust, employment exchange office, department for refugee affairs at the State Labour Commissariat and other government institutions of the Azerbaijan Soviet Socialist Republic. The court ordered him exiled to the Karelo-Finnish Soviet Socialist Republic (present day Karelia, northern Russia) to a correctional camp, where he died 9 years later.
A year later he was among the Azerbaijani politicians who were members of the Azerbaijani National Council who signed the Declaration of Independence of 28 May 1918 proclaiming Azerbaijan"s sovereignty, and became one of Members of Parliament of the newly founded state. Unlike many members of Musavat, Javad Malik-Yeganov did not choose to emigrate after the establishment of the Soviet rule in Azerbaijan. In 1933 he was accused of being a secret member of Musavat and arrested.