Arroyo was the starting quarterback for the San Jose Spartans between 1998 and 2002. He set many school records for passing, some of which are still unsurpassed. To this day, Arroyo ranks eighth in passing yards (4,603), ninth in completions (348) and total offense (4,525 yards), and tenth in passing efficiency (115.6). He still holds the school records for single-game passing efficiency and average yards per completion. Arroyo played in the NCAA Division I record setting game against Nevada in 2001, where he threw five touchdowns and the teams put up the score 64-45, which set the record for most total offense in a single game . Arroyo was the main-starter of the Spartans until Scott Rislov took the job in 2002. Arroyo graduated from San Jose State in 2003 with a degree in Kinesiology.
Following his playing career, Arroyo took a coaching position with San Jose State as an undergraduate assistant coach in 2003. The next year, he went to Prairie View A&M University where he served as the offensive coordinator. After one season in this capacity, Arroyo returned to San Jose State as a graduate assistant coach under newly hired head coach Dick Tomey. He was promoted to a full-time position in 2006, becoming the Spartans quarterbacks coach. Arroyo added co-offensive coordinator duties in 2007. During his tenure he worked with quarterbacks Adam Tafralis and Kyle Reed. After the 2008 season concluded, Arroyo accepted the position of offensive coordinator and quarterbacks coach at the University of Wyoming. He joined the University of California, Berkeley as quarterbacks coach in February 2011, adding the title of passing game coordinator prior to the 2012 season. In January 2013, Arroyo was hired by head coach Todd Monken as the offensive coordinator and outside receivers coach at Southern Miss. In January 2014, he was hired by head coach Lovie Smith to coach quarterbacks with the Tampa Bay Buccaneers. Arroyo left Tampa Bay in January 2015 and joined the Oklahoma State University football coaching staff in February 2015 as the running back coach. 
Marcus was Co offensive coordinator with Mario Cristobal for the Oregon Ducks in 2017. He will take over full interim offensive coordinator and play calling duties in The Las Vegas Bowl December,16 2017 for the Ducks under new Head Coach Mario Cristobal.