On October 27, 1988, Molina was at The Arco Arena in Sacramento, to challenge the IBF super featherweight champion Tony Lopez, in what marked the beginning of a three-fight rivalry between Molina and Lopez. Molina dropped Lopez in round two, but Lopez went on to retain the title by a split decision.

In his next fight, April 29, 1989, the WBO put him and former WBC featherweight champion Juan Laporte against each other for the vacant WBO super featherweight title. Molina became a world champion by beating Laporte by a 12-round unanimous decision at Roberto Clemente Coliseum in San Juan.

JOHN JOHN MOLINA VS:

1988-10-27    Tony Lopez I
1989-10-07    Tony Lopez II
1989-04-29    Juan Laporte
1990-01-28     Lupe Suarez II
1990-05-20    Tony Lopez III
1992-02-22     Jackie Gunguluza
1992-08-22     Fernando Caicedo
1993-02-13      Francisco Segura
1994-01-22      Floyd Havard
1994-04-22     Gregorio Vargas
1995-02-18      Oscar De La Hoya
1995-12-01       Eduardo Perez
1997-01-18      James Crayton I
1997-10-02     Joey Negron
1997-11-11       Moses James
1997-05-31      Elias Quiroz
1998-05-09     Shane Mosley
1999-01-16      Roberto Garcia
1999-03-20     Ruben Nevarez
1999-07-16     James Crayton II
2000-05-12     Emanuel Augustus