In the Name of the Rose by Umberto Eco is not set in Coimbra, but the medieval monastic atmosphere it evokes — labyrinthine libraries, Franciscan debates, the tension between learning and faith — is not far from the world that produced the Joanine Library.
Night Train to Lisbon by Pascal Mercier follows a Swiss academic who comes to Lisbon to trace the life of a Portuguese philosopher, but the themes of Portugal's hidden intellectual life, its dictatorships and its silences, illuminate the kind of country Coimbra's university has operated within for centuries.
The Last Kabbalist of Lisbon by Richard Zimler is a historical thriller set during the 1506 Lisbon Massacre, which touches on the fate of Portugal's Jewish community — a story also relevant to Coimbra, where the Inquisition was established and many conversos lived. Dark but compelling.