The team became the Houston Dynamo the following season, and he played a part in their MLS Cup wins in 2006 and 2007 before returning to the re-established Earthquakes in 2009.

Although he made only two MLS appearances for San Jose in 2005, he led the Earthquakes reserve team in scoring with eight goals in 12 games.

[7] Along with the rest of his Earthquakes teammates, he moved to Houston for the 2006 season and once again led the reserve team in scoring, tallying 13 goals in 11 games.

Wondolowski had a break-out season in 2010 in which he led Major League Soccer in scoring with 18 goals in 26 matches, leading San Jose into the MLS Playoffs.

NBC Sports Network aired an episode of MLS 36 following Wondolowski for 36 hours through his arrival in Philadelphia for the All-Star festivities and the game itself.

[citation needed] On October 6, 2012, Wondolowski became the San Jose Earthquakes' all-time leading goal-scorer at Colorado Rapids, a night where he notched his fourth career hat-trick.

[19] On August 24, 2014, Wondolowski became the only third MLS player to ever score double digit goal totals for five consecutive seasons, following the lead of Carlos Ruiz and Juan Pablo Angel.

[21] On May 24, 2015, Wondolowski drew a penalty against Orlando City SC at Levi's Stadium and scored his hundredth goal in MLS play.

[25] Wondolowski wore the number 38 in San Jose's U.S. Open Cup quarterfinal match on July 10, 2017, against the LA Galaxy in honor of teammate Matheus Silva, who nearly drowned the week before while swimming at Lake Tahoe.

[27] Wondolowski became the first player in league history to score 10 or more goals in 8 consecutive seasons on August 19, 2017, after converting an equalizing penalty in the final seconds of stoppage time in a 2–2 home draw against the Philadelphia Union, after Joshua Yaro brought down Shea Salinas in the box.

[28] On October 22, 2017, he received his seventh overall and fourth consecutive Team MVP award after finishing the 2017 regular season with 13 goals and 8 assists.

[32] Following his successful stint with the Earthquakes during the 2010 season which included winning the 2010 MLS Golden Boot, Wondolowski was called up to Winter Training Camp with the United States men's national soccer team.

At the conclusion of the three-week camp, his first cap with the national team came in a January 22, 2011, friendly against Chile at the Home Depot Center in Carson, California.

On February 1, 2014, Wondolowski added two more goals to his tally, by scoring a brace against South Korea at StubHub Center in Carson, California.

In the final minutes of regulation in what was then a 0–0 game,[36] Wondolowski failed to direct his shot on the net from just yards out and Belgium won in extra time.

He is of half Native American descent through his mother (Janis Hoyt) who was born into the Kiowa tribe from Oklahoma, of which Chris himself is also a member.

[45] In 2013, Wondolowski was named to the Division II 40th Anniversary Tribute Team, honoring his time spent at Chico State.