The Liberator by Eric Beerman covers Simón Bolívar's military campaign and the 1819 Battle of Boyacá fought just south of Tunja — the decisive engagement that broke Spanish rule in northern South America. Useful background for visiting the Puente de Boyacá.
El Carnero by Juan Rodríguez Freyle, written in the 1630s, is a gossipy chronicle of the colonial city of New Granada in its first century — full of duels, scandal, witchcraft, and political infighting. Some of the most memorable stories are set in Tunja. Hard to find in English; the Spanish original is widely available in Colombian bookshops.
Tunja: Capital de un Antiguo Reino by Eduardo Pinzón Cerón is the standard local history in Spanish, covering the Muisca origins, the Spanish conquest, and the colonial centuries in detail. Often available at the museum bookshops.
Affirmation of a Diocese: Tunja in the Sixteenth and Seventeenth Centuries by Jorge Tovar Pinzón is a scholarly study (English-language) of the early Catholic Church in Tunja, useful background for anyone who wants more depth than the church plaques provide.