Agoos arrived in San Jose in 2001 and helped kick off the best 5-year run in team history. In his first season with the Quakes, he led the team to their first ever MLS Cup Championship, while earning MLS Defender of the Year and MLS Best XI honors. In his four seasons, he was named an All-Star three times, while leading San Jose to four playoff berths and two MLS Cup titles. He also appeared in the 2002 FIFA World Cup during his tenure with San Jose.