Before the sultanate, the Tausug people lived in communities called banwa, each one essentially an independent city-state. Every banwa had its panglima, a leader chosen for political and physical strength, and its mangungubat, a healer who served as intermediary with the spiritual realm. These healers could be men or women and were exempt from traditional marriage customs, a social flexibility common across pre-Islamic and pre-Christian communities throughout the Philippine archipelago and northern Borneo. The Tausug traded with neighboring banwas, with the Digap of Malay, the Yakan of Basilan, and the nomadic Sama-Bajau seafarers who drifted through the archipelago's waters. Each banwa operated as a sovereign entity, making early Sulu less a unified state than a constellation of small, self-governing communities.

In 1280 AD, during the reign of Sipad the Younger, a figure named Tuan Masha'ikha arrived in Jolo. His origins remain obscure. Some accounts describe him as a Muslim who came "from foreign lands" leading a fleet of traders. Others say he emerged from a stalk of bamboo and was revered as a prophet. What is clear from the tarsila, the genealogical records of Sulu's ruling families, is that his arrival changed everything. He found the people of Maimbung worshipping tombs and stones. He preached Islam, married Sipad the Younger's daughter Idda Indira Suga, and fathered three children. From his lineage sprang a new aristocratic system called "tuanship," layered atop the existing rajahship. When Tuan Masha'ikha died in 1310 AD, he was buried at Bud Dato near Jolo, his grave inscribed with the name Tuan Maqbalu.

By the 1300s, Sulu had become a meeting point for peoples arriving from every direction. The Tagimaha, "the party of the people," came from Basilan and Mindanao. The Baklaya, "seashore dwellers" believed to have originated in Sulawesi, settled in Patikul. The Bajau sailed from Johor, blown off course by a monsoon, scattering to Sulu, Brunei, and Mindanao. These migrations created three distinct kingdoms with separate governments and subjects. According to Chinese annals from 1417, three kings ruled simultaneously: Paduka Batara governed the eastern kingdom across the Sulu Archipelago, Maharajah Kamal ud-Din controlled territory in Kalimantan, and the mysterious Paduka Patulapok reigned as the "Cave King" from Palawan. In 1365, the Majapahit Empire invaded Sulu. Four years later, the Sulus rebelled, counterattacked Brunei, and looted its capital of treasure and sacred pearls.

Islam arrived in waves. In 1380 AD, the Sufi scholar Karim ul-Makhdum reached Simunul Island from Malacca, the second Islamic preacher to visit after Tuan Masha'ikha a century earlier. He established a mosque in Tubig-Indangan, Simunul, the first in the Philippines, later known as Sheik Karimal Makdum Mosque. His travels across the Sulu Sea made him beloved in many communities; the people of Tapul built a mosque in his honor and claimed descent from him. Then in 1405, the Johore-born scholar Sharif ul-Hashim settled in Buansa, married a local princess named Paramisuli, and founded the Sultanate of Sulu. The rajahship, datuship, tuanship, and timwayship that had governed Lupah Sug for centuries were swept into a new Islamic order. By 1578, the sultanate had gained full independence from the Bruneian Empire, and Lupah Sug existed only in memory and genealogy.