The church of San Francesco sits near the top of the town, just below the Collegiata, and is one of Lucignano's two major medieval churches. Its Romanesque-Gothic facade is understated — plain stone and a pointed portal — but the interior holds genuine treasures.
The fresco cycle on the nave walls dates from the fourteenth century and depicts scenes from the lives of several saints. The quality is uneven, but the best fragments show the assured hand of painters working in the Sienese tradition. The church also preserves a carved stone sacristy doorway and several wooden choir stalls of considerable age.