The little-known Portuguese Chapel, also known as St Francis Xavier Chapel, is located on the seafront about 100 metres from the waterline at Shella area on Mama Ngina Road in Old Town, Malindi.
It is thatched with makuti and has a cross on top. It was built by Portuguese explorer Vasco Da Gama in 1498 while passing here on his way to India before St Francis Xavier visited Malindi in 1542.

It is said that St Francis Xavier passed through there with his two sailors who died and were buried at the chapel in 1542. The chapel, measuring five-by-five metres, has white walls that were made of coral rocks and sand. There is a security ‘window’ in one wall that was allegedly used to see enemies from the ocean. The church also has an altar with Catholic religious paraphernalia, two chairs and eight wooden benches on a cemented floor. It can accommodate 40 people seated and 50 to 60 standing.