Habib Husein, as the community knew him, drew followers quickly. People flocked to his settlement in Kampung Luar Batang, and the growing crowd attracted the suspicion of Dutch colonial authorities. Husein and his family were arrested and imprisoned in Glodok. What happened next belongs to local legend: according to the story, during every prayer time, Husein appeared to be leading prayers as imam in the communal holding room, even as prison guards confirmed he was simultaneously asleep in his locked cell. The miracle - or the reputation of it - secured his release. Husein continued preaching until his death on June 24, 1756, the 27th of Ramadan in the Islamic calendar. He was buried inside the mosque complex, where his tomb remains a site of pilgrimage. His lineage traces through the Ba'Alawi sada family to the Prophet Muhammad - a genealogy that reinforced his spiritual authority in a community that valued such connections deeply.

According to an inscription recorded on the mosque door in 1916, the building was completed on 29 April 1739 - the 20th of Muharram 1152 in the Islamic calendar. The village itself had been established earlier, around 1660, when the VOC relocated fishermen from East Java to the area. Their leader, Bagus Karta, received the honorary Dutch rank of lieutenant in 1677. The settlement grew on swampland that gradually solidified with sediment from the Ciliwung River. The mosque's qibla direction was imprecise - a common problem for early Southeast Asian mosques built before reliable methods for determining the bearing to Mecca were available. The scholar Muhammad Arshad al-Banjari corrected it during a stopover on his way home from the Hejaz to Banjar. Some scholars, including Abubakar Atjeh, have suggested that the original structure may have been Husein's own residence, later converted into a prayer hall.

By the 1870s, the mosque had become prosperous enough to provoke a dispute. The Perkara Luar Batang - the Luar Batang Affair - revolved around the substantial charity income the mosque collected. Two community leaders attempted to claim the funds, but their efforts were blocked by a fatwa from Habib Usman bin Yahya, who ruled that Husein's descendants held the rightful claim. In 1878, Ahmad Zayni Dahlan, the Grand Mufti of Mecca and a Shafi'i scholar, endorsed the fatwa - an extraordinary intervention that shows how connected Jakarta's Muslim community was to the broader Islamic world. The dispute nonetheless triggered quarrels among the local Arab community. On the advice of Christiaan Snouck Hurgronje, the Dutch government's influential advisor on Islamic affairs, the mosque courtyard was closed until an agreement could be reached. The affair dragged on until 1905, when a resolution was finally brokered.

The mosque's architecture carries its own symbolism. A large white gapura - a gate originally in the Javanese Hindu architectural tradition - marks the entrance to the complex. Inside, the square structure contains two large halls, each supported by twelve poles, for a total of twenty-four: the number of hours in a day, twelve of daylight and twelve of night. Beyond the outer hall lies the room containing Husein's tomb and that of his student, Haji Abdul Kadir. Renovations over the centuries have altered much of the original ornamentation, but the spatial logic persists. A curious account from 1791 adds another layer to the site's history. A Chinese explorer named Ong Hoe Hoe, visiting Batavia, wrote about a sage called Nek Bok Seng who lived in a wooden hut made of banana tree near what he described as 'the shrine.' Nek Bok Seng loved flute-playing, poetry, and chess. Whether this wise man was actually Habib Husein remains unresolved.

Today the mosque occupies roughly fourteen hectares of Kampung Luar Batang, about three kilometers from the old Arab quarter of Pekojan. It overlooks the port of Sunda Kelapa, where wooden pinisi schooners still dock alongside the concrete wharves - a view that connects the mosque to the maritime world that brought Husein here in the first place. The community considers the site keramat, sacred. Visitors come not only to pray but to pay respects at Husein's tomb, particularly during religious holidays when the kampung fills with pilgrims. The mosque is classified as a cultural heritage site of Jakarta, one of the oldest surviving Islamic structures in the city. Its walls have absorbed nearly three centuries of prayer, dispute, renovation, and devotion - a physical record of how Islam took root in a fishing village on the edge of a Dutch colonial capital and grew into something that outlasted the colony itself.