Duff began work on a catalogue of incunabula in the Bodleian Library but did not finish the project.
From 1893 to 1899, he compiled the first catalogue of the John Rylands Library, Catalogue of the Printed Books and Manuscripts in the John Rylands Library, Manchester (Manchester: J. E. Cornish, 1899).
Duff resigned from his position at the John Rylands Library in October 1900 and, for the rest of his life, he supported himself by doing freelance work and by taking academic appointments.
He was Sandars Reader in Bibliography at the University of Cambridge in 1903 and spoke on "The printers, stationers and book-binders of London, 1500–1535.
"[4][5] and again in 1911 speaking on "English provincial printers, stationers and book-binders to 1557."