[1] Based on the contents of the shipwreck, including an array of luxury items and currencies, archaeologist Dieter Noli and other scholars believe the ship was on course for western India from its home port in Lisbon, Portugal around the southern tip of Africa, a common route for similar Portuguese nau during this time that carried the same cargo.

[1] These naus commonly sailed between Portugal and China, India, and Japan, often carrying valuable and exotic cargo such as gold, copper, spices, ivory, weaponry, and silks to and from these markets.

[2] It is speculated that the Bom Jesus sank when it was pulled too closely to shore in a storm off the coast of Namibia, causing the ship's hull to collide with a rock and lean over, capsizing the vessel.

According to archaeologist Francisco Alves, the contents of the shipwreck were all covered in a moist, one meter-thick layer of "orange-layered concretion" built up from chemical, biological, and sedimentary processes in the coastal soil, helping to preserve much of the hull and wooden structure of the ship in the seawater-rich ground.

[3] A majority of the cargo was initially found scattered loosely between the three large digging sites, including copper ingots, ivory, nautical tools, and cannons that were easily dug out of the sand.

[3] Among the over 40 tons of cargo retrieved from the excavation site, thousands of different artifacts were recovered and cataloged, including cannons, firearms, swords, lead, tin, textiles, and astronomical devices.

The establishment of a Portuguese fort at the mouth of the Dahomey Gap in Benin in 1482 suggest that ivory hunted in this region was sent to the islands of Cape Verde and São Tomé to be processed before being shipped to Lisbon, where it would embark on its journey to Asian markets.

However, a lack of funding and permission from Namibian authorities has kept the ship's remains on-site in Oranjemund, storing a majority of the cargo and hull of the Bom Jesus in saltwater tanks for preservation until they can be safely transported.