Pereira was born in Vila Nova de Famalicão.

He arrived in China in 1672 and first stayed in the Portuguese colony of Macau, where he was enrolled in the University College of St. Paul.

Pereira was later sent to Beijing to work in the court of the Kangxi Emperor, where he stayed during most of his career.

In 1689, the Kangxi Emperor sent Pereira and his colleague Jean-François Gerbillon to interpret at the negotiations between Qing China and the Russian Empire in Nerchinsk, which eventually resulted in the Treaty of Nerchinsk.

He was buried in the Jesuits' Zhalan Cemetery in Beijing.