Ayala began his professional fighting career with a six round decision win over Jaime Olvera on November 27, 1992. He had seven fights in 1993, including one against veteran Jesse Magana. He won all seven, four by knockout. Magana himself was knocked out in the fourth round by Ayala.
In 1994, he won all four of his bouts, including one over veteran Lee Cargle, a man who has fought many other world champions and quality opponents himself. Cargle, who has travelled to many countries to fight many of the best fighters of the world, was beaten by Ayala with a knockout in round three.
1995 was a productive year for the young fighter. He won all five of his fights, including his first championship bout: He beat Mike Espinoza by knockout in three at Ft. Worth to claim the regional, North American Boxing Federation (NABF) Bantamweight title. He also defended that title twice before the end of the year, beating Mario Diaz and Sergio Millan, both by decision in 12 rounds.
In 1996, he only had two fights, both of them successful defenses of his regional belt: He knocked out Roland Gomez in seven rounds, and defeated Ivan Alvarez by decision in twelve.
He began 1997 by defeating Famosito Gomez by decision in twelve, once again retaining his belt. He won three more bouts that year, including a five round knockout over Roberto Lopez to retain the regional belt.
At the beginning of 1998, Ayala was already very close to a world championship bout. After winning two more bouts, he received his first chance at becoming world champion, when he travelled to Japan to challenge the WBC world Bantamweight champion Joichiro Tatsuyoshi on August 23. In a confusing outcome, Ayala lost that fight by a knockout in round seven, after the fight was stopped due to profuse bleeding by the challenger. While some said that the cut was produced by a punch, others said that it was actually produced by a headbutt (in which case they would have had to check the scorecards and declare the leading fighter winner by technical decision), but that the referee decided that the cut had been produced by a punch only because Tatsuyoshi was the local fighter. In any case, Ayala left his condition as an undefeated fighter in Japan the night he fought Tatsuyoshi.
After another win against Salazar, he began 1999 by beating David Vazquez by decision in ten. Then, he got his second chance at becoming a world champion, this time against WBA world Bantamweight champion Johnny Tapia, at Las Vegas, on June 26. He inflicted Tapia his first career loss and became world champion by beating Tapia with a twelve round decision in what turned out to be both Ayala's HBO Boxing debut and The Ring's fight of the year for 1999. He retained the title versus Saohin Sorthanicol before the end of that year.
Ayala began the new millennium basically right were he had left off the last one: He and Tapia met in a rematch, also telecast on HBO Boxing, July 10 of 2000. The WBA refused to recognize the bout as a world title bout, but it was fought for a title of a minor organization, the IBA, which is not regarded as a world title association by most boxing fans. He beat Tapia again, by twelve round decision. But prior to that, he had retained the title by a twelve round decision against the former world champion Johnny Bredahl, on March 4.
On March 30, 2001, Ayala recovered from a fourth round knockdown to retain his title with a 12 round decision against Hugo Dianzo in an ESPN telecast bout. His next two bouts were HBO telecasts, both against Clarence Bones Adams, a former world champion. The fights were recognized by the also not-highly regarded IBO. Ayala won both fights, held on August 4 of 2001 and on February 23 of 2002, by decision in twelve rounds.
Countinuing his rise in weight, Ayala on November 16 of 2002 met the WBC world Featherweight champion Erik Morales, this time coming on the losing end after 12 rounds by decision.
Ayala currently sports a record of 35 wins, 2 losses and 12 knockots as a boxer. He has stated, on his official website, that he remains committed to the Lord and to being a good example to his children and other kids.