| Friday, July 3, 2009 |
| TEAM |
 | Placed second baseman Kelly Johnson on the 15-day disabled list; purchased the contract of Brooks Conrad from Gwinnett of the International League (AAA). |
 | Placed second baseman Danny Richar on the 15-day disabled list; activated third baseman Edwin Encarnacion from the 60-day disabled list. |
 | Activated pitcher Claudio Vargas from the 15-day disabled list; transferred pitcher Hong-Chih Kuo from the 15-day to the 60-day disabled list. |
 | Activated pitcher Shawn Kelley from the 15-day disabled list; optioned first baseman Mike Carp to Tacoma of the Pacific Coast League (AAA). |
 | Recalled outfielder David Dellucci from Las Vegas of the Pacific Coast League (AAA); designated infielder/outfielder Russ Adams for assignment. |
| Thursday, July 2, 2009 |
| TEAM |
 | Acquired infielder Jeff Baker from the Colorado Rockies for pitcher Al Alburquerque; designated infielder Ryan Freel for assignment. |
 | Agreed to terms with free agent outfielder Wagner Mateo. |
 | Traded pitcher John Meloan to the Cleveland Indians for pitcher Winston Abreu. |
 | Signed catcher Santiago Nessy. |
| Wednesday, July 1, 2009 |
| TEAM |
 | Signed outfielder Reymond Fuentes. |
 | Reinstated catcher Yorvit Torrealba from the Major League restricted list; designated catcher Paul Phillips for assignment. |
 | Claimed infielder German Duran off of waivers from the Texas Rangers. |
 | Activated pitcher Eric Stults from the 15-day disabled list and optioned him to Alburquerque of the Pacific Coast League (AAA); optioned catcher A.J. Ellis to Alburquerque; designated outfielder Mitch Jones for assignment. |
 | Purchased the contract of outfielder Jeff Salazar from Indianapolis of the International League (AAA). |
 | Recalled infielder Jarrett Hoffpauir from Memphis of the Pacific Coast League (AAA); optioned pitcher Clayton Mortensen to Memphis. |
 | Optioned outfielder Elijah Dukes to Syracuse of the International League (AAA). |
| Tuesday, June 30, 2009 |
| TEAM |
 | Activated first baseman Chad Tracy from the 15-day disabled list; optioned pitcher Leo Rosales to Reno of the Pacific Coast League (AAA). |
 | Placed third baseman Mike Lowell on the 15-day disabled list, retroactive to Sunday; recalled infielder/outfielder Jeff Bailey from Pawtucket of the International League (AAA). |
 | Recalled pitcher Jeff Samardzija from Iowa of the Pacific Coast League (AAA); optioned pitcher Jose Ascanio to Iowa. |
 | Released pitcher Luis Vizcaino. |
 | Activated pitcher Mike Hampton from the 15-day disabled list; optioned pitcher Wesley Wright to Round Rock of the Pacific Coast League (AAA); signed pitchers Dallas Keuchel and Max Fearnow. |
 | Placed pitcher Antonio Bastardo on the 15-day disabled list, retroactive to Friday; recalled pitcher Sergio Escalona from Lehigh Valley of the International League (AAA). |
 | Acquired outfielder/catcher Eric Fryer and pitcher Casey Erickson from the New York Yankees for outfielder Eric Hinske; purchased the contract of outfielder Garrett Jones from Indianapolis of the International League (AAA); acquired outfielder Lastings Milledge and pitcher Joel Hanrahan from the Washington Nationals for outfielder Nyjer Morgan and pitcher Sean Burnett. |
 | Placed third baseman Adrian Beltre on the 15-day disabled list, retroactive to Monday; sent catcher Jamie Burke outright to Tacoma of the Pacific Coast League (AAA); purchased the contract of outfielder Ryan Langerhans from Tacoma. |
| Monday, June 29, 2009 |
| TEAM |
 | Recalled outfielder Sam Fuld from Iowa of the Pacific Coast League (AAA); placed second baseman Aaron Miles on the 15-day disabled list, retroactive to June 21. |
 | Activated pitcher Chris Perez; optioned second baseman Josh Barfield to Columbus of the International League (AAA); signed pitcher Antwonie Hubbard. |
 | Recalled pitcher Lucas French from Toledo of the International League (AAA); optioned pitcher Alfredo Figaro to Toledo. |
 | Recalled outfielder Travis Buck from Sacramento of the Pacific Coast League (AAA); optioned third baseman Jack Hannahan to Sacramento. |
 | Placed shortstop Khalil Greene on the 15-day disabled list; purchased the contract of pitcher Clayton Mortensen from Memphis of the Pacific Coast League (AAA). |
 | Recalled outfielder Julio Borbon from Oklahoma City of the Pacific Coast League (AAA); optioned pitcher Willie Eyre to Oklahoma City. |
 | Activated pitcer Scott Olsen from the 15-day disabled list; optioned pitcher Shairon Martis to Syracuse of the International League (AAA); agreed to terms with second baseman Jeffrey Kobernus, pitchers Chad Jenkins Daniel Rosenbaum, Brandon King, Matt Swynenberg and Shane McCatty and shortstop Kyle Breault. |
| Sunday, June 28, 2009 |
| TEAM |
 | Placed pitcher Koji Uehara on the 15-day disabled list, retroactive to Wednesday; recalled pitcher David Hernandez from Norfolk of the International League (AAA). |
 | Activated infielder Asdrubal Cabrera from the 15-day disabled list. |
 | Placed pitcher Nate Robertson on the 15-day disabled list, retroactive to Saturday; recalled pitcher Fu-Te Ni from Toledo of the International League (AAA). |
 | Activated third baseman Geoff Blum from the 15-day disabled list; optioned second baseman Edwin Maysonet to Round Rock of the Pacific Coast League (AAA); agreed to terms with pitcher Dallas Keuchel. |
 | Activated second baseman Mark Ellis from the 60-day disabled list; optioned first baseman Daric Barton to Sacramento of the Pacific Coast League (AAA); transferred pitcher Josh Outman to the 60-day disabled list. |
 | Placed first baseman Rich Aurilia on the bereavement list; recalled pitcher Ryan Sadowski from Fresno of the Pacific Coast League (AAA); placed pitcher Kelvin Pichardo on the 60-day disabled list. |
 | Placed pitcher Matt Harrison on the 15-day disabled list; recalled pitcher Tommy Hunter from Oklahoma City of the Pacific Coast League (AAA). |
 | Activated pitcher Roy Halladay from the 15-day disabled list; optioned pitcher Brad Mills to Las Vegas of the Pacific Coast League (AAA). |
 | Traded outfielder Ryan Langerhans to the Seattle Mariners for infielder Mike Morse; activated pitcher Scott Olsen from the 15-day disabled list; optioned pitcher Shairon Martis to Syracuse of the International League (AAA). |
| Saturday, June 27, 2009 |
| TEAM |
 | Optioned pitcher Billy Buckner to Reno of the Pacific Coast League (AAA); recalled pitcher Leo Rosales from Reno. |
 | Agreed to terms with pitcher Matt Hobgood. |
 | Recalled pitcher Homer Bailey from Louisville of the International League (AAA); optioned infielder Adam Rosales to Louisville. |
 | Activated pitcher Jose Veras; optioned pitcher Jensen Lewis to Columbus of the International League (AAA); signed pitcher Kyle Smith. |
 | Activated pitcher Felipe Paulino from the 15-day disabled list; designated pitcher Brandon Backe for assignment. |
 | Purchased the contract of pitcher Bruce Chen from Omaha of the Pacific Coast League (AAA). |
 | Activated pitcher Eric Milton from the 15-day disabled list; optioned pitcher Cory Wade to Albuquerque of the Pacific Coast League (AAA). |
 | Acquired infielder/outfielder Mark DeRosa from the Cleveland Indians for pitcher Chris Perez and a player to be named. |
 | Optioned pitcher Andy Sonnanstine to Durham of the International League (AAA); designated pitcher Winston Abreu for assignment; activated pitchers Scott Kamir and Chad Bradford from the 15-day disabled list. |