Although the Roman occupation has long been attested, it was between the years 2009 and 2014, during excavations in this parish, that was discovered a Roman villa, now known as the Roman Villa of Corte. This villa was the first building complex of the Roman period, located in the Algarve barrocal area, and the most important structure of this period, excavated in the Algarve region.
Under Muslim rule from the 8th century to the 12th century, it was previously known as Mussiene prior to its recapture from the Moors by the Kingdom of Portugal during the Reconquista, in 1189. During the period before the conquest by the troops of king Sancho I of Portugal and the crusaders, the parish of São Bartolomeu de Messines was then called Mussiene, a toponym of Arabic origin which derives from the Arabic word mâzin, which means complimentary.