The Portuguese ship was involved in the hugely lucrative spice trade between Portugal and India, the municipal council in Cascais, a town near Lisbon, said.
Peppercorns, cowry shells used in the slave trade and bronze artillery pieces litter the wreck site.
The wreck was found last month during dredging at the mouth of the River Tagus, on Portugal’s Atlantic coast, the council said in a statement.
Preliminary excavations have also found porcelain dating from the period of China’s Wanli Emperor in the late 16th and early 17th centuries.
The find came during an offshore mapping project compiling an inventory of wrecks.