The youngster has put pen to paper on a new deal at the Etihad and has subsequently joined up with Uwe Rosler's Latics as they look to gain promotion to the Premier League
The Wales international made his competitive debut in last season's FA Cup win over Blackburn and spent the second half of the 2013-14 campaign on loan at Birmingham, winning the club's Player of the Month award in his first month at the club.
The 20-year-old will now hope to continue his development at the DW Stadium under Uwe Rosler as the Latics look to return to the top-flight.
“Emyr is a great talent of this club which he proved on loan at Birmingham City last year – he showed that he can play at Championship level but this time it will be a different challenge.
“Whereas last year, he was fighting against relegation with Birmingham, this time he’s going to a club expecting to win and aiming to win promotion, so I’m really pleased he’s both agreed to stay on at City until 2016 and that he’s taken this opportunity Wigan have offered him.”