| 3. Round | 24/05/2009 | Houston Dynamo | - | San Jose Earthquakes | 3:1 | ||||
| 3. Round | 28/05/2009 | Columbus Crew | - | San Jose Earthquakes | 2:1 | ||||
| 3. Round | 31/05/2009 | San Jose Earthquakes | - | Real Salt Lake | 2:1 | ||||
| 4. Round | 07/06/2009 | FC Dallas | - | San Jose Earthquakes | 2:2 | ||||
| 4. Round | 14/06/2009 | Seattle Sounders | - | San Jose Earthquakes | 2:1 | ||||
| 5. Round | 04/07/2009 | Real Salt Lake | - | San Jose Earthquakes | 1:1 |  |
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| 5. Round | 12/07/2009 | San Jose Earthquakes | - | Toronto FC | 1:3 | ||||
| 5. Round | 19/07/2009 | Chicago Fire | - | San Jose Earthquakes | 2:0 | |
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| 5. Round | 26/07/2009 | San Jose Earthquakes | - | D.C. United | 2:2 | |
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| 6. Round | 02/08/2009 | San Jose Earthquakes | - | Seattle Sounders | 4:0 | |
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| 6. Round | 09/08/2009 | San Jose Earthquakes | - | Columbus Crew | 0:3 | ||||
| 6. Round | 23/08/2009 | San Jose Earthquakes | - | Kansas City Wizards | 1:0 | |
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| 7. Round | 19/09/2009 | San Jose Earthquakes | - | Colorado Rapids | 1:1 | ||||
| 7. Round | 24/09/2009 | Colorado Rapids | - | San Jose Earthquakes | 1:1 | ||||
| 7. Round | 27/09/2009 | D.C. United | - | San Jose Earthquakes | 1:2 | ||||
| 8. Round | 10/10/2009 | Toronto FC | - | San Jose Earthquakes | 1:1 |
USA