After a fire during the night of Good Friday in 1670 destroyed the roof and part of the interior of the Basilica Cattedrale di Santa Margherita in Montefiascone, the repair and completion of the construction was entrusted to Fontana.
[3] Innocent XII commissioned Fontana to extend the Ospizio Apostolico di San Michele complex, organized around its church.
Fontana was an able artist and a good designer, but lacked the innovation that characterized early Baroque architects like Cortona and Borromini.
By order of Pope Innocent XI, he wrote a diffuse historical description of the Templum Vaticanum (1694), which included his project for completing St. Peter's.
In this work Fontana advised the demolition of that dense nest of medieval houses called La Spina which formed a sort of island from Ponte Sant'Angelo to the piazza of St. Peter's; the project was completed under Benito Mussolini, creating the Via della Conciliazione.
Among Fontana's disciples, who spread his fame throughout Europe, were Giovanni Battista Vaccarini in Sicily, Filippo Juvarra in Italy and Spain, James Gibbs in England, Matthäus Daniel Pöppelmann in Germany, Johann Lucas von Hildebrandt and Fischer von Erlach in Austria, Nicodemus Tessin the Younger in Sweden, and Nicola Michetti in Italy and Russia.