The town has existed since Roman times, when it was called Beatia.
In the Middle Ages Baeza was a flourishing Moorish city, said to contain 50,000 inhabitants, but it fell to the forces of Ferdinand III of Castile in 1227. The Jaén and Úbeda gates, and the arch of Baeza, are among the remains of its Moorish fortifications.
In the 16th century, Baeza and nearby Úbeda grew rich from the production of textiles, and local nobles hired important architects, such as Andrés de Vandelvira, to design new palaces, churches and public squares in the fashionable Italian style. The economy collapsed in the 17th century, which had the fortunate side effect of preserving Baeza's Renaissance architectural legacy, because few newer structures were built.