Before he became Vatican librarian, he was director of the grand-ducal press of Tuscany and professor of ecclesiastical history and controversy in the Sapienza.
He is the author of several treatises about art and artists. Amongst his works is Dialoghi sopra le tre Arti del Disegno, published in Lucca, 1754. In these dialogues he criticizes the role of patrons, who "understand little of art" (Dialoghi II & III). He was also principal editor of the new edition of the Vocabulario della Crusca and of the celebrated Vatican edition of Virgil (1741).
Bottari was acquainted to Piranesi. He probably collaborated on Piranesi's answers to the letters of Pierre-Jean Mariette, and Piranesi dedicated his Antichità Romane de' Tempi della Repubblic to Bottari.