After missing games in both the 2014 and 2015 MLS Cup Playoffs, Alonso was being actively shopped around the league by the Seattle Sounders front office due to durability concerns before the start of the 2016 MLS season. A trade did not materialize, and Alonso went on to make 38 league and playoff appearances for the 2016 MLS Cup winning Sounders. He picked up an injury during the playoffs for the third season in a row during the second leg of the Western Conference Finals against the Colorado Rapids when a collision led to a sprained knee. Alonso played through the injury, playing all 120 minutes of the 2016 MLS Cup Final in a penalty shootout win over Toronto FC. He required four pain killing injections before the Final and another four injections at half time to make it through the game. Head coach Brian Schmetzer praised Alonso for his determination and service to the club after the victory.