A sole winless season followed in 2005 with Factory Honda Team and Biaggi was replaced by Dani Pedrosa for 2006 even though he got 4 podiums and a 5th place in the championship.

The following season, Biaggi joined Honda, and finished fourth in the championship standings, including a single victory in Barcelona.

Biaggi made an impressive start in his 500cc debut, qualifying on pole, setting the fastest lap and winning his first race in the 1998 Japanese motorcycle Grand Prix at Suzuka, riding for the Kanemoto Honda team.

He was also victorious at the Czech Republic Grand Prix, where he almost crashed when he accidentally did a 90° wheelie,[9] and finished the season in second place behind Mick Doohan.

He won in Brno, Czech Republic[10] and Sepang, Malaysia[11] to clinch runner-up in the championship behind rival Valentino Rossi.

In 2003, Biaggi finished third in the MotoGP championship after rejoining Honda on the Camel Pramac Pons team and won races in Pacific Grand Prix[12] and Great Britain after Rossi penalised.

[15] At the end of the 2004 MotoGP season Biaggi finished the championship in third place, behind Sete Gibernau and series winner, Rossi.

It was hoped that continued cooperation with Kanemoto and the full factory support from Honda would make Biaggi one of the main title contenders in 2005.

Biaggi attempted to reach an agreement to race the Superbike World Championship for Corona Alstare Suzuki in 2006, but the team could not commit to equal equipment with their existing riders, 2005 champion Troy Corser and Yukio Kagayama.

After a hard championship Biaggi finished third, behind World Champion James Toseland and Yamaha top rider Noriyuki Haga.

At the end of the season, Francis Batta, Alstare Suzuki Racing Team director, was forced to release Biaggi, due to the loss of the main sponsor Corona Extra, as they could not reach financial agreement.

He took a double podium in round 2 at Qatar, and scored solid points before taking their first win since the return at Brno, after race leaders Fabrizio and Ben Spies collided.

Biaggi continued with Aprilia for 2010, taking a double victory at the team's home race at Monza to move up to second in the standings.

Even though he was in contention for the title due to multiple second-place finishes, Biaggi fractured his left foot in Germany which caused him to miss 2 rounds: Imola and Magny Cours.

[27] All stats according to MotoGP.com[28] (key) (Races in bold indicate pole position, races in italics indicate fastest lap) (key) (Races in bold indicate pole position, races in italics indicate fastest lap) Giacomo Agostini, Hideo Kanaya, Kenny Roberts, Eddie Lawson, Wayne Rainey, John Kocinski, Luca Cadalora, Norifumi Abe, Max Biaggi, Valentino Rossi, Jorge Lorenzo, Ben Spies, Maverick Viñales, Fabio Quartararo 1949  B. Ruffo 1950  D. Ambrosini 1951  B. Ruffo 1952  E. Lorenzetti 1953  W. Haas 1954  W. Haas 1955  H. Müller 1956  C. Ubbiali 1957  C. Sandford 1958  T. Provini 1959  C. Ubbiali 1960  C. Ubbiali 1961  M. Hailwood 1962  J. Redman 1963  J. Redman 1964  P. Read 1965  P. Read 1966  M. Hailwood 1967  M. Hailwood 1968  P. Read 1969  K. Carruthers 1970  R. Gould 1971  P. Read 1972  J. Saarinen 1973  D. Braun 1974  W. Villa 1975  W. Villa 1976  W. Villa 1977  M. Lega 1978  K. Ballington 1979  K. Ballington 1980  A. Mang 1981  A. Mang 1982  J. Tournadre 1983  C. Lavado 1984  C. Sarron 1985  F. Spencer 1986  C. Lavado 1987  A. Mang 1988  S. Pons 1989  S. Pons 1990  J. Kocinski 1991  L. Cadalora 1992  L. Cadalora 1993  T. Harada 1994  M. Biaggi 1995  M. Biaggi 1996  M. Biaggi 1997  M. Biaggi 1998  L. Capirossi 1999  V. Rossi 2000  O. Jacque 2001  D. Kato 2002  M. Melandri 2003  M. Poggiali 2004  D. Pedrosa 2005  D. Pedrosa 2006  J. Lorenzo 2007  J. Lorenzo 2008  M. Simoncelli 2009  H. Aoyama 2010  T. Elías 2011  S. Bradl 2012  M. Márquez 2013  P. Espargaró 2014  T. Rabat 2015  J. Zarco 2016  J. Zarco 2017  F. Morbidelli 2018  F. Bagnaia 2019  Á. Márquez 2020  E. Bastianini 2021  R. Gardner 2022  A. Fernández 2023  P. Acosta 2024  A. Ogura