In the late 1980s, the Portuguese Government of Macao at the time discovered archaeological remains in the Ruins of St. Paul, during an investigation project conducted on the site. Meanwhile, it was decided that the Macao Museum would be constructed at Mount Fortress, and further remains were found in this area. The matters gave rise to two excavation projects on both places between 1988 and 1992, and between 1995 and 1996, respectively. During the excavation work, a large number of archaeological remains were discovered, as were remains of structures belonging to the old College of St. Paul. The findings served as important references for the analysis of the original architectural plan and functions of the church and college of St. Paul, as well as for the restoration and musealization works that were to be undertaken.
Between 2010 and 2012, in line with a government-led comprehensive development study for the area around the Ruins of St. Paul, the Cultural Affairs Bureau invited some archaeologists from Mainland China to carry out the ‘Archaeological Investigation and Excavation Project of the Ruins of St. Paul's College’. The focus was on the site, on Rua de D. Belchior Carneiro, close to the remains of the Church of the College of St. Paul. The project brought fruitful results, particularly the discovery of a large man-made trench with numerous ceramic pieces and thousands of blue and white porcelain fragments. They included many fragments of Kraak porcelain (Kraakporselein), presumably manufactured in the late Ming and early Qing dynasties (from late 16 century to mid-17 century) for export sale.
The great number of Kraak porcelain pieces uncovered in the project, together with those unearthed in different parts of Macao since the 1990s, offer archaeological evidence of Macao having been a key transhipment port and trade hub on the Maritime Silk Road of the time. In light of the importance of this excavation project, the Cultural Affairs Bureau reinforced the protection of the archaeological site, preserving the remains of the man-made pit inside a protective bamboo structure.