[3][2] Abbot's studies were chiefly in Southwest Asian languages and textual criticism of the New Testament, though his work as a bibliographer showed such results as the exhaustive list of writings (5300 in all) on the doctrine of the future life, appended to W. R. Alger's History of the Doctrine of a Future Life, as it has prevailed in all Nations and Ages (1862), and published separately in 1864.

[3][2] Abbot's publications, though always of the most thorough and scholarly character, were to a large extent dispersed in the pages of reviews, dictionaries, concordances, texts edited by others, Unitarian controversial treatises, etc.

However, he took a more conspicuous and personal part in the preparation (with Baptist scholar Horatio Balch Hackett) of the enlarged American edition of Dr. (afterwards Sir) William Smith's Dictionary of the Bible (1867–1870), to which he contributed more than 400 articles, as well as greatly improving the bibliographical completeness of the work.

[4] His principal single work, representing his scholarly method and conservative conclusions, was The Authorship of the Fourth Gospel: External Evidences (1880; 2nd ed.

In spite of the compression due to its form, this work was up to that time probably the ablest defense, based on external evidence, of the Johannine authorship, and certainly the most complete treatment of the relation of Justin Martyr to this gospel.