Allen struggled at times during training camp. Teammate and veteran tight end Antonio Gates envisioned that Allen in 2013 would play behind Eddie Royal, Vincent Brown, Malcom Floyd, and Danario Alexander. Although Alexander suffered a season-ending injury in the preseason, Allen did not participate in any offensive plays in San Diego's season opening loss to the Houston Texans. Unaccustomed to being a reserve player, he considered quitting football and returning to school to complete his degree. He began receiving playing time the following week against the Philadelphia Eagles when Floyd suffered a season-ending injury. On October 6, 2013, against the Oakland Raiders, Allen had his first 100-yard game as an NFL receiver, having six catches for 115 yards and a touchdown. The next week, in a win against the Indianapolis Colts on Monday Night Football, Allen recorded nine catches for 107 yards and a touchdown. In Week 14, he broke the franchise record for receptions in a rookie season, surpassing LaDainian Tomlinson, with 61 with three weeks remaining in the regular season.