In 2002, he signed with the MetroStars of Major League Soccer. In 2003, he moved to the Portland Timbers of the USL First Division. On September 29, 2004, the Chicago Storm of the Major Indoor Soccer League (MISL) traded Kevin Sakuda to the San Diego Sockers for the rights to Alvarez. On October 18, 2004, the Storm signed him on loan from the Timbers and he played the 2004–2005 and 2005–2006 indoor seasons in Chicago. Following the 2006 USL-1 season, Alvarez became a free agent and on April 3, 2007 signed with the Charleston Battery of USL-1. He played twenty-two games and scored eight goals. On July 9, 2007, the Monterrey La Raza of MISL selected Alvarez in the MISL expansion draft. The LaRaza went to the MISL championship series, but fell to the Baltimore Blast. Following the end of the indoor season, he contacted Gavin Wilkinson, coach of the Timbers, about the possibility of rejoining the Timbers. Alvarez signed with the Timbers on July 14, 2008. He played only nine games with the Timbers and returned to the LaRaza which was now playing in the newly created National Indoor Soccer League. On April 7, 2009, he was announced as the 2008-09 NISL Most Valuable Player.

On October 25, 2010 The Missouri Comets announced they had signed Byron Alvarez to play in their first season back in the MISL. Alvarez was vital to the Comets run to the MISL playoffs, leading the team and the league in scoring with 80 points. Alvarez also led the league in goals scored (33), hat tricks (5) and tied for the league-lead in game-winning goals with five. Alvarez scored at least one point in 17 games this season and he also posted the longest goal-scoring streak of the year (nine games) and point-scoring streak (15 games). He capped off this great season by being named 2010–2011 MISL MVP.