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However, Mendes Leal's tenure was frequently interrupted by other responsibilities, and in his absence, decisions were made by António da Silva Túlio. Túlio, a writer and historian, had been working at the National Library since 1844 in various capacities, including as an official, curator, and librarian, in succession, eventually serving as interim director in the absence of the chief librarian.
In organisational terms, the library did not undergo significant changes and was divided into three departments: Sciences and Arts, History and Literature, Manuscripts and Numismatics. Major changes came with António José Enes, who succeeded Mendes Leal as director in September 1886. During his tenure, the Inspeção das Bibliotecas e Arquivos Públicos [Inspection of Public Libraries and Archives] was established (29 December 1887), consisting of an inspector from the National Library and another from the Torre do Tombo. This body was responsible for creating a collective catalogue, promoting inter-library loans, and developing technical training for librarians and archivists.
Up to this date, the literary and economic administration of the National Library of Lisbon (BNL) had been overseen by a Council supervised by the chief librarian. This changed with the establishment of the Inspeção Geral das Bibliotecas e Arquivos Públicos [General Inspection of Public Libraries and Archives], and remained thus until the reorganisation introduced by the decree of 24 December 1901, which strengthened the supervisory power of the chief librarian, placing him directly under the Ministry of the Kingdom and granting him broad authority over public libraries. The position of director was created for the BNL, who was responsible for general administration, compliance with regulations, and executing all orders from the chief librarian, to whom he was required to report quarterly on the library's services.
The technical changes implemented during the brief tenure of António Enes resulted in a different organisational structure for Libraries and Archives, with new nomenclatures, as well as the establishment of the librarian-archivist course, in which he taught the bibliology module. A graduate of the Curso Superior de Letras, a journalist, playwright, and co-author of a History of Portugal, Enes was particularly known for his work in the field of colonial politics. He used this promotion, facilitated by his progressive comrades, to dedicate himself more to library science.
