After several impressive displays he secured a move to giants FC Porto. Under the management of former England boss Bobby Robson, Emerson won successive league titles, appeared in the European Champions League, and won the 1996 Portuguese player of the year award. By now, Emerson had grown in stature and attracted notable interest from major European clubs, with him going to Middlesbrough F.C. of the FA Premier League.
Middlesbrough's iconic manager Bryan Robson's challenge to win Boro their first honour ultimately convinced Emerson to choose the Premiership side over four other Italian Serie A clubs and completed a controversial £4 million move in 1996. The deal was done behind Bryan Robson's back by the club president, Robson only finding out by accident after it was unwittingly mentioned by Boro chief scout Ray Train in conversation.
However, things turned sour quickly. With FC Barcelona manager Bobby Robson expressing his interest in bringing Emerson to the Camp Nou. This unsettled the midfielder, already having endured relegation to Division One and with his wife unable to settle on Teesside. He travelled to Brazil for a break at the end of 1997, but once in Brazil he threatened he would never return.
He eventually moved to CD Tenerife in January 1998 for around £4.25 million after the dispute, although on surprisingly good terms, Boro chief executive Keith Lamb stating he had tried to re-sign him after Tenerife were relegated. He remained with the Canary Islands club until 2000 when he moved to Deportivo de La Coruña.
After further stays with Atlético Madrid and Rangers F.C. (he became the first ever Brazilian to play for Rangers), Emerson moved to Greece, joining Skoda Xanthi in the summer of 2005. After having stayed there for only 6 months, he transferred to AEK Athens FC, in January 2006.On May 23, 2007 Emerson was released by AEK to join 2007 Cyprus champions, APOEL FC, from Nicosia.
He received Portuguese citizenship after he married his Portuguese wife.