Visible for miles around, the Basilica di San Francesco is the crowning glory of Assisi's Unesco-listed historic centre. The 13th-century complex is comprised of two churches: the Gothic Basilica Superiore, with its celebrated cycle of Giotto frescoes, and beneath, the older Basilica Inferiore where you'll find works by Cimabue, Pietro Lorenzetti and Simone Martini. Also here, in the Cripta di San Francesco, is St Francis' much-venerated tomb.
Perched on the forested slopes of Monte Subasio, this monastery is set around the caves where St Francis and his followers prayed and contemplated spiritual matters. The carceri (isolated places, or 'prisons') are as peaceful today as in St Francis' time, even though they're now surrounded by religious buildings. It's a claustrophobic walk down to Francesco's Grotta (cave), where he prayed and slept on a stone bed in his later years.
This spot is known as a "little bit fancy, a little bit trendy" with great pasta.
For those wanting a hike, this is a difficult loop that is about ~3k total vertical feet and 12 mi. But, you can do however much you would like. The route runs clockwise on paths and with breathtaking views, crossing beautiful colored valleys and a beautiful view of Assisi. The route starts from Assisi and passes from Colle San Rufino (1110m), from the Vallonica Refuge, from the Fonte Bregno Refuge and on the way back you pass by the Eremo delle Carceri.
Apparently good meringue and good espresso.