The church of Santa Margherita, which occupies a magnificent position in the upper part of Cortona, is constructed over an oratorio built originally by order of this Franciscan penitent nun and dedicated to St Basil, St Aegidius and St Catherine of Alexandria. The oratorio built by order of St Margherita was in turn erected over the remains of a small church built in the 11th century by the Camaldolensian monks and dedicated only to St Basil.
After St Margherita’s death in 1297, the inhabitants of Cortona ordered a larger church in her honour to be built alongside the original church dedicated to St Basilio, behind which the saint had spent the last years of her life in isolation in a small room. This larger church was designed by Giovanni Pisano and decorated with frescoes of the Senese School. In 1330 the remains of the saint were moved here, from their original resting place in San Basilio.