Among the buildings he designed was St John the Baptist Church, Norwich, which in 1976 was to become a Roman Catholiccathedral. He was also responsible for buildings in the Cambridge colleges of Christ's, Pembroke and Peterhouse. He masterminded the main buildings of Dulwich College in South London. Some of his finest works, the churches of All Hallows, Southwark (1877), and St Agnes, Kennington (1880) were destroyed by bombing.
Scott was an alcoholic and suffered mental ill health. He was declared of unsound mind in 1884, but following moving to France, he was declared sane again and continued his architectural work from Rouen. He died from cirrhosis of the liver in a bedroom of the Midland Grand Hotel, which was designed by his father.