Khomyakov came from a family that had for many generations served the Russian tsars. He received an excellent education and acquired a mastery of numerous languages. Though he did not enroll as a student, Aleksey passed his final examinations in mathematics at Moscow University. A visit to France for 18 months completed his education.

During the Russo-Turkish War (1828–29) he served with distinction, and he spent the remainder of his life in Moscow involved in intellectual pursuits, though frequently visiting his family estates of Bugucharovo and Lipitsy. He was reputed to have been happily married and had several children.

Khomyakov was known as a gifted writer and a brilliant controversialist; he dealt with a wide range of subjects, composed poetry, and wrote philosophical and political essays and treatises on economics, sociology, and theology. A successful landlord, he was also a self-taught doctor who treated many of the peasants on his estates.

Rigid censorship in tsarist Russia permitted only some of his articles to appear in print during his lifetime. His major theological and historical works were thus published posthumously by his friends and associates.

Khomyakov belonged to what has been called the Golden Age of Russian literature. At that time (first half of the 19th century) an intellectual elite of exceptional ability created a striking contrast to the proponents of the reactionary rule of Nicholas I (1825–55). The best Russian thinkers were preoccupied with the problem of the political and social orientation of their people. Russia had been brought out of its previous isolation by Peter I the Great (1682–1725), and contacts with the West had stimulated the upper classes, but under Nicholas I they felt frustrated and dissatisfied. Two main groups appeared in response to this situation: the Westernizers (Westernizer) and the Slavophiles (Slavophile). The Westernizers saw in the political institutions of the West and in liberal and socialist ideas a pattern for imitation. The Slavophiles, led by Khomyakov, insisted that Russia should follow its own path of development based on the pre-Petrine (pre-Peter the Great) culture inspired by the Eastern Orthodox church.

Though Khomyakov felt at home in the Western world, he also knew and loved Russia's past, a sentiment rare among his upper-class contemporaries. His aim was to combine the best elements of both traditions, but the social system he advocated was opposed to the individualism of the West. He did not believe that secularized and selfish man, denying the existence of a divine creator, could establish a satisfactory political and social order. Criticizing both capitalism and socialism, he regarded them as coming from the same Western outlook. He believed that the root of man's problems lay in what he viewed as the defects of Western interpretations of Christianity, and he blamed Roman Catholicism and Protestantism equally for their failure to solve the problem of the relationship between authority and freedom. “Rome kept unity at the expense of freedom. Protestants had freedom but lost unity.” He was convinced that the Orthodox church possessed a more balanced presentation of Christian teaching than any of the Western churches. Indeed, Khomyakov's contribution to the movement was chiefly in the field of theology, rather than through political nationalism.

In Khomyakov's system the key term was sobornost, a word with a number of broad translations, among them “togetherness” and “symphony.” This word, in the Slavonic version of the Nicene Creed, corresponds to “catholic.” It does not, however, mean “universal” but denotes a perfect organic fellowship of redeemed people united by faith and love. Khomyakov believed that a person could best achieve spiritual and intellectual maturity in an organic community that respected the liberty of its members and that true progress would depend not on competition (as in the West) but on cooperation. He thus claimed that the task of the church was to teach mankind how to live in unity and freedom. In Khomyakov's estimation, the Christian West, after its separation from the East, had not been able to fulfill this role. His writings on sobornost are among the more influential of his works.

In another aspect of his Slavophile thought, Khomyakov idealized the Russian peasants, exalted their humility and sense of brotherhood, and regarded them as better fitted to realize a Christian social order than the more aggressive Western nations.

Khomyakov's vast erudition, his literary gifts, his integrity, and his strength of convictions should have procured for him a distinguished political and academic career. But he lived under the oppressive rule of Nicholas I and had no opportunity of using his talents for the public good. He remained until his death a mere retired cavalry captain. He died from cholera, which he caught from the peasants whom he treated.