The church's prominence continued under Dutch rule after they captured Malacca from the Portuguese in 1641. The Dutch repurposed the building for Protestant services, naming it "Bovenkerk" (Upper Church). However, when Christ Church was built in 1753, the Church of Saint Paul fell into disuse and gradually decayed.
Today, the Church of Saint Paul stands in ruins, but its skeletal structure offers a glimpse into Malacca's colonial past. The church's strategic hilltop location provides panoramic views of the city and the Strait of Malacca. Notable features include the tombstones of early European settlers and the statue of St. Francis Xavier, who used the church as a temporary burial site before his body was moved to Goa, India.
The Church of Saint Paul is a testament to the layers of Malacca's history, reflecting its Portuguese, Dutch, and British colonial eras. It remains a popular tourist attraction, symbolizing the historical confluence of European and Asian cultures in Malaysia.