- Colorado Rockies signed Daryl Boston of the New York Mets as a free agent on December 21, 1992.
- Colorado Rockies signed Howard Johnson of the New York Mets as a free agent on November 19, 1993.
- New York Mets signed free agent Chris Jones of the Colorado Rockies on December 7, 1994.
- New York Mets traded Bret Saberhagen and David Swanson to the Colorado Rockies for Juan Acevedo and Arnold Gooch on July 31, 1995.
- New York Mets traded Jerry Dipoto to the Colorado Rockies for Armando Reynoso on November 27, 1996.
- Colorado Rockies signed Lenny Harris of the New York Mets as a free agent on November 9, 1998.
- Colorado Rockies signed Jim Tatum of the New York Mets as a free agent on December 18, 1998.
- New York Mets traded Brian McRae, Rigo Beltran and Tom Johnson to the Colorado Rockies for Darryl Hamilton and Chuck McElroy on July 31, 1999.
- New York Mets traded Masato Yoshii to the Colorado Rockies for Bobby Jones and Lariel Gonzalez on January 14, 2000.
- New York Mets signed free agent Kurt Abbott of the Colorado Rockies on January 26, 2000.
- Colorado Rockies signed Billy Taylor of the New York Mets as a free agent on February 4, 2000.
- Colorado Rockies signed Mike Hampton of the New York Mets as a free agent on December 9, 2000.
- New York Mets traded Mark Leiter to the Colorado Rockies for Brian Rose on March 27, 2001.
- New York Mets traded Gary Bennett to the Colorado Rockies for Ender Chavez on August 23, 2001.
- Colorado Rockies signed Rick White of the New York Mets as a free agent on January 10, 2002.
- New York Mets traded Todd Zeile and Benny Agbayani to the Colorado Rockies for Alex Ochoa, Craig House and Ross Gload on January 21, 2002.
- New York Mets traded Corey Brittan to the Colorado Rockies for Kane Davis on February 21, 2002.
- New York Mets traded Jay Payton, Mark Corey and Robert Stratton to the Colorado Rockies for John Thomson and Mark Little on July 31, 2002.
- Colorado Rockies signed Steve Reed of the New York Mets as a free agent on January 19, 2003.
- New York Mets traded Kazuo Matsui to the Colorado Rockies for Eli Marrero on June 9, 2006.
- New York Mets signed free agent Cory Sullivan of the Colorado Rockies on January 20, 2009.
- New York Mets signed free agent Livan Hernandez of the Colorado Rockies on February 14, 2009.
- Colorado Rockies signed Tim Redding of the New York Mets as a free agent on January 27, 2010.
- Colorado Rockies signed John Maine of the New York Mets as a free agent on February 17, 2011.
- New York Mets signed free agent Carlos Torres of the Colorado Rockies on November 15, 2012.
- New York Mets traded Collin McHugh to the Colorado Rockies for Eric Young on June 18, 2013.
- Colorado Rockies signed Greg Burke of the New York Mets as a free agent on November 6, 2013.
- Colorado Rockies signed LaTroy Hawkins of the New York Mets as a free agent on November 22, 2013.
- New York Mets signed free agent Michael Cuddyer of the Colorado Rockies on November 10, 2014.
- Colorado Rockies signed John Lannan of the New York Mets as a free agent on November 18, 2014.
- Colorado Rockies signed Omar Quintanilla of the New York Mets as a free agent on January 27, 2015.
- New York Mets signed free agent Kevin Pillar of the Colorado Rockies on February 21, 2021.
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