He graduated at Bowdoin College in 1840; and in 1847, at the request of Prof. Andrews Norton, went to Cambridge, where he was principal of a public school until 1856. He was assistant librarian of Harvard University from 1856 to 1872, and planned and perfected an alphabetical card catalogue, combining many of the advantages of the ordinary dictionary catalogues with the grouping of the minor topics under more general heads, which is characteristic of a systematic catalogue. From 1872 until his death he was Bussey Professor of New Testament Criticism and Interpretation in the Harvard Divinity School.
His studies were chiefly in Oriental languages and the 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. His 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, &c.; but he took a more conspicuous and more personal part in the preparation (with the Baptist scholar, Horatio B. 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 besides greatly improving the bibliographical completeness of the work; was an efficient member of the American revision committee employed in connexion with the Revised Version (1881-1885) of the King James Bible; and aided in the preparation of Caspar Rene Gregory's Prolegomena to the revised Greek New Testament of Tischendorf. His principal single production, representing his scholarly method and conservative conclusions, was The Authorship af the Fourth Gospel: External Evidences (1880; second edition, by J. H. Thayer, with other essays, 1889), originally a lecture, and in spite of the compression due to its form, up to that time probably the ablest defence, based on external evidence, of the Johannine authorship, and certainly the completest treatment of the relation of Justin Martyr to this gospel.
Abbot, though a layman, received the degree of S. T. D. from Harvard in 1872, and that of D.D. from Edinburgh in 1884. He died in Cambridge, Massachusetts, on the 21st of March 1884.