His work in reorganizing the manuscript department was of lasting value, and to him is due the classified catalogue of manuscripts, and the improved efficiency and punctuality of publication of the department. In 1873, he was appointed principal librarian of the British Museum. Under his supervision, the new buildings of the White Wing were erected, to accommodation prints, drawings, manuscripts and newspapers. The purchase of the Stowe manuscripts was concluded while he was in office. He founded, in conjunction with Sir Edward Maunde Thompson, the Palaeographical Society, and made scientific improvements to classical palaeography.
He was made LL.D. of Cambridge in 1879, created CB in 1885, and KCB the day before his death in January 1898. Bond published little, but he was the editor of four volumes of facsimiles of Anglo-Saxon charters from 679 to the Conquest, The Speeches in the Trial of Warren Hastings (1859–1861), and a number of other historic documents.