Ethnically Belarusian, Alyaksandr Malinouski was born into a rural teacher's family. While working on his medical degree at Moscow University, he was arrested for joining the paramilitary revolutionary group, Narodnaya Volya. He was briefly exiled to Tula. He resumed his medical studies at the University of Kharkiv (Ukraine), where he became involved in revolutionary activities and published his "Brief course of economic science" in 1897. In 1899, he graduated as a medical doctor, and published his next work, "Basic elements of the historical perspective on nature". He was arrested by the Tsar's police, spent six months in prison, and was exiled to Vologda.

In his pursuit of social justice, Malinouski studied political philosophy and economics, took the pseudonym Bogdanov, and in 1903 joined the Bolshevik faction of the Russian Social Democratic Labor Party. For the next six years Bogdanov was a major figure among the early Bolsheviks, second only to Vladimir Lenin in influence. In 1904 - 1906, he published three volumes of the philosophic treatise Empiriomonizm, in which he tried to merge Marxism with the philosophy of Ernst Mach, Wilhelm Ostwald, and Richard Avenarius. His work later affected a number of Russian Marxist theoreticians, including Nikolai Bukharin. In 1907, he helped organize the 1907 Tiflis bank robbery with both Lenin and Leonid Krasin.

For four years after the collapse of the Russian Revolution of 1905, Bogdanov led a group within the Bolsheviks ("ultimatists" and "otzovists" or "recallists"), who demanded a recall of Social Democratic deputies from the State Duma, and he vied with Lenin for the leadership of the Bolshevik faction. By mid 1908, the factionalism with the Bolsheviks had become irreconcilable. A majority of Bolshevik leaders either supported Bogdanov or were undecided between him and Lenin. Lenin concentrated on undermining Bogdanov's reputation as a philosopher. In 1909 he published a scathing book of criticism entitled Materialism and Empiriocriticism, assaulting Bogdanov's position and accusing him of philosophical idealism. In June 1909, Bogdanov was defeated by Lenin at a Bolshevik mini-conference in Paris organized by the editorial board of the Bolshevik magazine Proletary, and expelled from the Bolsheviks.

He joined his brother-in-law Anatoly Lunacharsky, Maxim Gorky, and other "otzovists" on the island of Capri, where they started a school for Russian factory workers. In 1910, Bogdanov, Lunacharsky, Mikhail Pokrovsky, and their supporters moved the school to Bologna, where they continued teaching classes through 1911, while Lenin and his allies soon started a rival school outside of Paris. Bogdanov broke with the "otzovists" in 1911 and abandoned revolutionary activities. After six years of his political exile in Europe, Bogdanov returned to Russia in 1914, following an amnesty.

Bogdanov's innovative work on the comparative study of economic and military power of European nations, written in 1912 - 1913, was the first interdisciplinary work ever on systems analysis, which he later merged with tectology. Bogdanov discovered what have become modern principles of systems theory and systems analysis, although his research remained unknown to systems theory posterity until many decades after his death. His works on systems analysis were not translated in his lifetime.

During World War I Bogdanov served as a physician at a hospital. He had no involvement in the Russian Revolution of 1917. After the Bolshevik seizure of power in October 1917, Bogdanov refused multiple offers to rejoin the party and denounced the new regime as similar to Aleksey Arakcheyev's arbitrary and despotic rule in the early 1820s.

In 1918, Bogdanov became a professor of economics at the University of Moscow and director of the newly established Socialist Academy of Social Sciences.

In 1918 - 1920, Bogdanov cofounded the proletarian art movement Proletkult and was its leading theoretician. In his lectures and articles, he called for the total destruction of the "old bourgeois culture" in favour of a "pure proletarian culture" of the future. At first Proletkult, like other radical cultural movements of the era, received financial support from the Bolshevik government, but by 1920 the Bolshevik leadership grew hostile and on December 1, 1920 Pravda published a decree denouncing Proletkult as a "petit bourgeois" organization operating outside of Soviet institutions and a haven for "socially alien elements". Later in the month the president of Proletkult was removed and Bogdanov lost his seat on its Central Committee. He withdrew from the organization completely in 1921 - 1922.

In the summer of 1923, Bogdanov was arrested by the Soviet secret police on suspicion of having inspired the recently discovered secret oppositionist group Worker's Truth. He was soon released.

In 1924, Bogdanov started his blood transfusion experiments, apparently hoping to achieve eternal youth or at least partial rejuvenation. Lenin's sister Maria Ulianova was among many who volunteered to take part in Bogdanov's experiments. After undergoing 11 blood transfusions, he remarked with satisfaction on the improvement of his eyesight, suspension of balding, and other positive symptoms. The fellow revolutionary Leonid Krasin wrote to his wife that "Bogdanov seems to have become 7, no, 10 years younger after the operation". In 1925 - 1926, Bogdanov founded the Institute for Haemotology and Blood Transfusions, which was later named after him. But a later transfusion cost him life, when he took the blood of a student suffering from malaria and tuberculosis. Some scholars (e.g. Loren Graham) have speculated that his death may have been a suicide, because Bogdanov wrote a highly nervous political letter shortly beforehand, while others attribute it to blood type incompatibility, which was poorly understood at the time.

Bogdanov wrote science fiction to test out his political - scientific ideas. Most of Bogdanov's works remain unavailable in English.

In 1908, Bogdanov published the novel, Red Star about a utopia set on Mars. In it, he made predictions about future scientific and social developments. His utopia also dealt with feminist themes, which would become more common in later utopian science fiction, e.g., the two sexes becoming virtually identical in the future, or women escaping "domestic slavery" (one reason for physical changes) and being free to pursue relationships with the same freedom as men, without stigma. Other notable differences between the utopia of Red Star and present day society include workers having total control over their working hours, as well as more subtle differences in social behavior such as conversations being patiently "set at the level of the person with whom they were speaking and with understanding for his personality although it might very much differ from their own". The novel also gave a detailed description of blood transfusion in the Martian society.

Red Star was one of the inspirations for Red Mars, an award winning science fiction novel by Kim Stanley Robinson. Bogdanov is the surname of the character Arkady, who is also a fictional descendant of Alexander Bogdanov. Bogdanov later published a prequel to Red Star, called Engineer Menni (1913).

He seems to have had in mind a third book during the composition of the poem, "A Martian Stranded on Earth" (1924).

From 1913 until 1922, Bogdanov immersed himself in the writing of a lengthy philosophical treatise of original ideas, Tectology: Universal Organization Science. Tectology anticipated many basic ideas of Systems Analysis, later explored by Cybernetics. In Tectology, Bogdanov proposed to unify all social, biological, and physical sciences by considering them as systems of relationships and by seeking the organizational principles that underlie all systems. His three volume book anticipated many ideas later popularized by Norbert Wiener in Cybernetics and Ludwig von Bertalanffy in General Systems Theory. Both Wiener and von Bertalanffy may have read the German translation of Tectology, published in 1928. In Russia, Lenin (and later Stalin) considered Bogdanov's natural philosophy an ideological threat to dialectic materialism. The rediscovery of Tectology occurred only in the 1970s.

Both Bogdanov's fiction and his political writings imply that he expected the coming revolution against capitalism to lead to a technocratic society. This was because the workers lacked the knowledge and initiative to seize control of social affairs for themselves as a result of the hierarchical and authoritarian nature of the capitalist production process. However, Bogdanov also considered that the hierarchical and authoritarian mode of organization of the Bolshevik party was also partly to blame, although Bogdanov considered at least some such organization necessary and inevitable.

In the 1920s and 1930s, Bogdanov's theorizing, being the product of a non-Leninist Bolshevik, became an important, though "underground", influence on certain dissident factions in the Soviet Union who turned against Bolshevik autocracy while accepting the necessity of the Revolution and wishing to preserve its achievements.