On Christmas Eve 1886, Ingram resigned as Librarian and took up office as the Senior Lecturer. He was later elected Vice-Provost of the College and President of the Royal Irish Academy, and he remained active in research and publication for more than a decade. He was succeeded as Librarian on 29 January 1887 by Thomas Kingsmill Abbott, a Junior Fellow. (See Figure 16.) Abbott resigned as Professor of Biblical Greek at the end of 1888, but he retained his other Chair, that of Hebrew, alongside the Librarianship, until 1900. He quickly began to address the problems of storage that were again becoming acute, and during his tenure of office he immersed himself in the Library's collections, compiled catalogues and greatly expanded the collection of objects on display in the Long Room. The day-to-day running of the Library was left largely in the hands of the senior Assistant Librarians.

The first of those, Thomas French, died in 1889 and the Board again considered whether he should be replaced by a Junior Fellow, for whom the post could be seen as an apprenticeship for the post of College Librarian. Abbott wrote a lengthy memorandum against the proposal, arguing that the management of the Library between the time of Barrett and that of Todd, when the Assistant Librarian had been a Junior Fellow, provided no justification to follow that example. Indeed, he said, the Library was still suffering ‘from the perfunctory manner in which some of the Librarians of that time performed their duties’. He conceded that, though Todd – the exception to his criticism – had been both a Junior Fellow and the Assistant Librarian, he was ‘only nominally so; he was really Acting Librarian and owed nothing to training under his Chief’. The Board was persuaded and Thomas Keenan, the junior Assistant Librarian, succeeded French. Samuel Brambell, a Library clerk, was promoted to be the junior Assistant Librarian and Alfred de Burgh, who had graduated from Trinity a decade earlier, was appointed as a second junior Assistant Librarian.