La Concha Bay was home to the most important port of the Kingdom of Navarre in the 11th and 12th centuries. A papal bull from 1096 mentions the parish of San Sebastián on the shore, in what is now El Antiguo. In 1101, a previous donation of this church and its properties to the monastery of Leire was confirmed. Among the listed properties in the 12th century were several nasas, large wooden and net funnel-like traps used to catch fish at the mouth of the Igara stream, on Ondarreta beach. Also included was a pardina, a farming and livestock estate in the Town of Itzurun, in what is now the Old Town (Parte Vieja), near the natural harbor at the base of Mount Urgull.
This thriving port settlement of Itzurun had two parishes: Santa María and San Vicente, both still present today and mentioned as early as the late 12th century—though likely older. Burials from the 10th century linked to Santa María were found in the nearby convent of Santa Teresa, along with traces of Roman-era habitation.
The Town of Itzurun became the seat of the town of San Sebastián, granted town status by King Sancho VI the Wise of Navarre around 1180, making it the oldest town in Gipuzkoa. The founding charter served as a commercial regulation, allowing San Sebastián to flourish as a maritime power with jurisdiction over the entire coastal strip of the Kingdom of Navarre, from the Bidasoa to the Oria rivers. Economic and political power was reinforced by religious and military presence: in the 12th century, the Augustinian convent of San Bartolomé—the oldest in Gipuzkoa—was founded, and a fortification was built atop Mount Urgull, the origin of today’s Castillo de la Mota. Despite these defenses, in 1200 Castile took the castles, the town, and its territories.