Being, as he said, eager to arrive at "the truth without bias and prejudice, and free from partisan spirit," he determined to accept the results of his investigation, even if they conflicted with Karaite teachings and traditions.
This work was the "Mibhar" (The Choice), a commentary on the Pentateuch, written in the terse, concise, and often obscure style and after the critical method of Ibn Ezra, and this became to the later generation of Karaite teachers a source of instruction in religious philosophy, in exegesis, and in practical theology, that is, the observance of the Torah.
Prophecy he explains as a psychological, not a physical, process, manifested in different forms; either the inner eye or ear perceiving the object in a vision or dream, or, the truth being on a higher plane, communicated intuitively.
Aaron is very outspoken on the subject of man's free will, opposing emphatically the notion held by ibn Ezra and others, that human destiny or disposition is influenced by the planets.
His conception of the human soul is peculiar and probably influenced by his medical studies: it seems to him in its various functions dependent upon the brain, the blood, and the spinal cord or marrow; whereas otherwise he claims full independence for the immortal spirit.
It was his "Seder Tefillot" (Book of Prayers and Hymns) that was adopted by most of the Karaite congregations as the standard prayer-book, and that probably earned for him the epithet "ha-Kadosh" (the Saint).
He also composed a didactic poem, presenting in brief rimes for popular instruction and education the contents and spiritual lessons of each weekly portion of the Pentateuch.
He wrote, also, a grammar under the title of "Kelil Yofi" (Diadem of Beauty), a compilation from older works, with his own additions, among which was a chapter on Bible exegesis; but he left it unfinished.