The Commissioner's Cup is a rotating trophy awarded to the institution that garners the most overall all-sports' points during the year.
2018-19 Commissioner's Cup Standings
| Place | School | Men's | Women's | Total |
| 1. | Hanover | 77.50 | 78.17 | 155.67 |
| 2. | Rose-Hulman | 76.50 | 67.33 | 143.83 |
| 3. | Transylvania | 58.84 | 78.33 | 137.17 |
| 4. | Franklin | 56.16 | 53.50 | 109.66 |
| 5. | Earlham | 47.83 | 49.50 | 97.33 |
| 6. | Anderson | 42.17 | 50.51 | 92.68 |
| 7. | Mount St. Joseph | 34.18 | 52.50 | 86.68 |
| 8. | Manchester | 46.17 | 40.50 | 86.67 |
| 9. | Bluffton | 28.50 | 30.66 | 59.16 |
| 10. | Defiance | 30.16 | 25.00 | 55.16 |
2017-18 Commissioner's Cup Standings
| Place | School | Men's | Women's | Total |
| 1. | Rose-Hulman | 74.5 | 67.5 | 142.0 |
| 2. | Hanover | 60.0 | 65.0 | 125.0 |
| 3. | Transylvania | 41.8 | 62.3 | 104.2 |
| 4. | Franklin | 49.8 | 53.3 | 103.1 |
| 5. | Manchester | 49.5 | 48.3 | 97.8 |
| 6. | Earlham | 42.3 | 39.2 | 81.5 |
| 7. | Mount St. Joseph | 40.2 | 40.7 | 80.8 |
| 8. | Bluffton | 31.0 | 38.0 | 69.0 |
| 9. | Anderson | 41.5 | 21.7 | 63.2 |
| 10. | Defiance | 28.3 | 26.0 | 54.3 |
Past HCAC Commissioner's Cup Winners
| Year | School | Points |
| 18-19 | Hanover | 155.67 |
| 17-18 | Rose-Hulman | 142.0 |
| 16-17 | Rose-Hulman | 137.3 |
| 15-16 | Rose-Hulman | 130.3 |
| 14-15 | Rose-Hulman | 130.3 |
| 13-14 | Rose-Hulman | 128.5 |
| 12-13 | Franklin | 126.7 |
| 11-12 | Transylvania | 112.0 |
| 10-11 | Transylvania | 107.66 |
| 09-10 | Rose-Hulman | 96.0 |
| 08-09 | Franklin | 95.5 |
| 07-08 | Rose-Hulman | 103.0 |
| 06-07 | Anderson | 92.5 |
| 05-06 | Manchester | 81.0 |
