| | | Sunday, September 22nd, 2013 | | Signed SP Ryan Graves to a 3-year contract extension worth a total of $11,281,500. |
| Saturday, September 21st, 2013 | | Signed CL Aurelio Cortés to a 3-year contract extension worth a total of $28,980,000. |
| Sunday, July 21st, 2013 | | Signed Iván López to a minor league contract with a signing bonus of $660,000. |
| Thursday, June 20th, 2013 | | Signed Bryant Jones to a minor league contract with a signing bonus of $180,000. |
| Monday, June 17th, 2013 | | Signed Carlos Ramírez to a minor league contract with a signing bonus of $550,000. |
| Saturday, June 8th, 2013 | | Signed SP Julius Montgomery to a 2-year contract extension worth a total of $2,990,000. | | Signed MR Earl Mercer to a 2-year contract extension worth a total of $2,323,000. |
| Monday, May 20th, 2013 | | 2B Phil Brown was designated for assignment and placed on waivers. | | Placed MR Earl Mercer on the active roster. | | Activated MR Earl Mercer from the 60-day disabled list. |
| Saturday, December 8th, 2012 | | MR Peter Roberts was designated for assignment and placed on waivers. | | Placed MR Earl Mercer on the active roster. |
| Wednesday, December 5th, 2012 | | Signed free agent MR Earl Mercer to a 1-year contract worth a total of $1,010,000. |
| Sunday, November 18th, 2012 | | RF Kurt McKinney received a 1-year contract through automatic renewal worth a total of $400,000. | | SP Nicholas Long received a 1-year contract through automatic renewal worth a total of $400,000. | | SS Yin-fat Yuan received a 1-year contract through automatic renewal worth a total of $400,000. | | 1B Lonnie Gómez received a 1-year contract through automatic renewal worth a total of $400,000. | | 2B Arthur Hendrickson received a 1-year contract through automatic renewal worth a total of $400,000. | | SP Ãngel Acevedo received a 1-year contract through automatic renewal worth a total of $400,000. | | SP Jack Abrams received a 1-year contract through automatic renewal worth a total of $400,000. | | SP Michael Ryan received a 1-year contract through automatic renewal worth a total of $400,000. | | SP Monty Skinner received a 1-year contract through automatic renewal worth a total of $400,000. | | C Dave Steele received a 1-year contract through automatic renewal worth a total of $400,000. | | C Domingo MartÃnez received a 1-year contract through automatic renewal worth a total of $400,000. | | LF Octávio Pérez becomes a free-agent. | | LF Mario MartÃnez received a 1-year contract through automatic renewal worth a total of $400,000. | | MR Jesús Rosário becomes a free-agent. | | 1B Joe Palk received a 1-year contract through automatic renewal worth a total of $400,000. |
| Thursday, November 15th, 2012 | | 3B Mark Puckett received a 1-year contract through arbitration worth a total of $8,500,000. | | SS Santiago Rivera received a 1-year contract through arbitration worth a total of $600,000. | | CF Javier López received a 1-year contract through arbitration worth a total of $600,000. | | MR Santiago Sánchez received a 1-year contract through arbitration worth a total of $850,000. | | MR Julius Montgomery received a 1-year contract through arbitration worth a total of $1,300,000. | | 2B Phil Brown received a 1-year contract through arbitration worth a total of $600,000. | | MR Manuel Alcorta becomes a free-agent. | | SP Héctor Brito received a 1-year contract through arbitration worth a total of $600,000. | | C Albert Patton received a 1-year contract through arbitration worth a total of $600,000. |
| Thursday, October 25th, 2012 | | MR John Black has executed his last optional contract year. |
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