| 2024-11-16 | UFC 309: Jones vs. Miocic | Bantamweight | Marcus McGhee def. Jonathan Martinez | Decision (unanimous) (29–28, 29–28, 29–28) | 3 | 5:00 |
| 2024-05-04 | UFC 301: Pantoja vs. Erceg | Bantamweight | José Aldo def. Jonathan Martinez | Decision (unanimous) (30–27, 30–27, 30–27) | 3 | 5:00 |
| 2023-10-14 | UFC Fight Night: Yusuff vs. Barboza | Bantamweight | Jonathan Martinez def. Adrian Yañez | TKO (leg kick) | 2 | 2:26 |
| 2023-03-11 | UFC Fight Night: Yan vs. Dvalishvili | Bantamweight | Jonathan Martinez def. Said Nurmagomedov | Decision (unanimous) (29–28, 29–28, 29–28) | 3 | 5:00 |
| 2022-10-15 | UFC Fight Night: Grasso vs. Araújo | Bantamweight | Jonathan Martinez def. Cub Swanson | TKO (leg kick) | 2 | 4:19 |
| 2022-05-21 | UFC Fight Night: Holm vs. Vieira | Bantamweight | Jonathan Martinez def. Vince Morales | Decision (unanimous) (30–27, 30–27, 30–27) | 3 | 5:00 |
| 2022-02-26 | UFC Fight Night: Makhachev vs. Green | Featherweight | Jonathan Martinez def. Alejandro Pérez | Decision (unanimous) (29–28, 29–28, 30–27) | 3 | 5:00 |
| 2021-10-23 | UFC Fight Night: Costa vs. Vettori | Bantamweight | Jonathan Martinez def. Zviad Lazishvili | Decision (unanimous) (30–27, 29–28, 29–28) | 3 | 5:00 |
| 2021-03-13 | UFC Fight Night: Edwards vs. Muhammad | Bantamweight | Davey Grant def. Jonathan Martinez | KO (punch) | 2 | 3:03 |
| 2020-10-18 | UFC Fight Night: Ortega vs. The Korean Zombie | Featherweight | Jonathan Martinez def. Thomas Almeida | Decision (unanimous) (30–27, 30–27, 30–27) | 3 | 5:00 |
| 2020-08-01 | UFC Fight Night: Brunson vs. Shahbazyan | Catchweight | Jonathan Martinez def. Frankie Saenz | TKO (knee and punches) | 3 | 0:57 |
| 2020-02-08 | UFC 247: Jones vs. Reyes | Bantamweight | Andre Ewell def. Jonathan Martinez | Decision (split) (28–29, 29–28, 30–27) | 3 | 5:00 |
| 2019-07-13 | UFC Fight Night: de Randamie vs. Ladd | Bantamweight | Jonathan Martinez def. Liu Pingyuan | KO (knee) | 3 | 3:54 |
| 2019-02-10 | UFC 234: Adesanya vs. Silva | Bantamweight | Jonathan Martinez def. Wuliji Buren | Decision (unanimous) (30–27, 30–27, 29–28) | 3 | 5:00 |
| 2018-10-27 | UFC Fight Night: Volkan vs. Smith | Bantamweight | Andre Soukhamthath def. Jonathan Martinez | Decision (unanimous) (30–26, 29–28, 29–28) | 3 | 5:00 |