The defender started 31 of Sporting's 38 La Liga matches last season, but could not prevent Los Rojiblancos from being relegated to the Segunda Division.
Malaga were said to lead the race for the 20-year-old, but Koln have swooped to land a player that has also previously been linked with a move to Barcelona.
"I'm really looking forward to Cologne and proving myself in the Bundesliga and the Europa League," Mere told the German club's official website. "It's a club where young players can develop themselves. There were plenty of rumours, but my aim was always to join Koln."
Mere had represented Sporting since the age of 13, and revealed last weekend that he would depart the club with a heavy heart.
Koln finished fifth in the Bundesliga table last season.