I remembered reading about one particular visit which I thought was the Italian, Pigafetta in 1521 talking about a five layer mosque in Kampong Ayer but I was corrected that it was actually a Spanish, Alonso Beltran who described the mosque in 1578. But in June later that year, the Spanish attacked Brunei and burnt the mosque to the ground. What they wanted to do was burn the mosque and burn the spirits of the Muslim Bruneians. However they were mistaken, the Bruneians rose up and drove the Spanish out a few days later.
The news of the burning of the great Muhammad's mosque in Borneo was delivered to King Philip II of Spain. Again the Spanish was wrong thinking that this would weaken the Muslims but by the reign of Sultan Hassan, the Bruneian missionaries had been able to spread Islam to Suluk, Cuyo, Kermaian and Mindano. In Brunei itself, the mosque was rebuilt. A Spanish report in 1590 had the following report:
"...they have a mosque, which they called Massaguit; and there they come to commend themselves to Allah, which they call to and Mahoma, who they say is his procuratior so that with God they do not urge much. The common people go to the mosque and thw women never go but it is the men. They have water at the door of mosque. With that they wash their feet. There three kinds of religious men although they differ not in habit from those who are not. They called these catif..."
A number of other mosques have been built. Even during the civil wars between Sultan Abdul Mubin and Sultan Muhyiddin, Sultan Abdul Mubin built a mosque in Pulau Cermin. In the later years, during the reign of Sultan Omar Ali Saifuddien II, the main mosque was built in Kampung Bendahara Lama. It was used until the reign of Sultan Abdul Mumin. Sultan Hashim Jalilul Alam, the 25th Sultan built a mosque at Kampung Cina (now Kampung Kianggeh). Sultan Muhammad Jamalul Alam II built the first one on dry land calling it Masjid Marbut Pak Tunggal and later known as Masjid Pekan Brunei. This one lasted until it was destroyed during the 2nd World War.
During that time, two citizens volunteered their houses to be the main mosque. One was Pehin Orang Kaya Digadong Awang Yusof in Kampung Sumbiling and later Pengiran Pemancha Anak Haji Mohd Yassin. By then the government had built a temporary mosque called Masjid Kajang as everything was made up of leaves and timber. Almost all the mosques built in Brunei at that time was voluntarily done. Most of them did not survive, one was at Jalan Gadong, Pekan Muara, Masjid Thambi at Labu Estate Temburong, even the Masjid Pekan Seria (built by Brunei Shell). It was in 1958 when the Masjid Sultan Omar Ali Saifuddien was finally built.