| Snake Eaten | Platinum (PlayStation only) | FOXHOUND | 12. Run 2: Extreme, the FOXHOUND Run |
| Young Gun | Bronze | A story trophy that pops during the scenes at Rassvet. | 1. Run 1: The Virtuous Mission |
| Pain Relief | Bronze | The fight with The Pain | 4. Run 1: The Crevice and the Caves |
| If It Bleeds, We Can Kill It | Bronze | The fight with The Fear | 5. Run 1: Ponizovje and Graniny Gorki |
| The End | Bronze | The fight with The End | 6. Run 1: Svyatogornyj and Sokrovenno |
| Houston, We HAD a Problem | Bronze | The fight with The Fury | 7. Run 1: Krasnogorje and the Underground Tunnel |
| River of Pain | Bronze | The fight with The Sorrow | 9. Run 1: Groznyj Grad Sewers to Tikhogornyj |
| Grounded | Bronze | The fight with Volgin | 10. Run 1: The Hangar to Rokovoj Bereg |
| Shagadelic | Bronze | The fight with the Shagohod | 10. Run 1: The Hangar to Rokovoj Bereg |
| The Patriot | Bronze | The fight with The Boss | 10. Run 1: The Hangar to Rokovoj Bereg |
| Like a Boss | Bronze | The trophy for finishing the game on any difficulty. | 11. Run 1: The Results Screen |
| Mama Said | Bronze | Earned for knocking a guard out with a CQC slam. | 1. Run 1: The Virtuous Mission |
| Tell Me Where the Bomb Is | Bronze | Earned for interrogating a guard with CQC. | 1. Run 1: The Virtuous Mission |
| Like He Just Doesn't Care | Bronze | Earned for holding up a guard. | 1. Run 1: The Virtuous Mission |
| Close Shave | Bronze | Earned for cutting a guard's throat in a CQC hold. | 1. Run 1: The Virtuous Mission |
| Don't Touch the Sides | Bronze | The trophy for digging a bullet out of Snake with the knife in the Cure menu. | 10. Run 1: The Hangar to Rokovoj Bereg |
| Can I Keep It? | Bronze | Earned for catching any animal alive. | 1. Run 1: The Virtuous Mission |
| Snake Eater | Bronze | Earned for eating a snake of any kind. | 1. Run 1: The Virtuous Mission |
| I Can Totally See You | Bronze | Earned for a camo index of 90% or more. | 1. Run 1: The Virtuous Mission |
| A Good Man Is Hard to Find | Bronze | The trophy for a camouflage index of 100%. | 6. Run 1: Svyatogornyj and Sokrovenno |
| Snake Bit | Bronze | Earned for poisoning a guard with a live venomous animal. | 2. Run 1: Dremuchij to Rassvet |
| Serenity Now | Bronze | Earned for calling one Healing Radio station: a hidden frequency that plays a song and tops up stamina. | 1. Run 1: The Virtuous Mission |
| Tune-In Tokyo | Bronze | Earned for calling every Healing Radio station of the difficulty you are on. | 1. Run 1: The Virtuous Mission |
| Beekeeper | Bronze | Earned for setting hornets on a guard. | 1. Run 1: The Virtuous Mission |
| Just Because | Bronze | The trophy for blowing up a munitions shed with TNT. | 3. Run 1: Chyornyj Prud and Bolshaya Past |
| Mostly Dead | Bronze | Earned for taking the Fake Death Pill, which you start with. | 1. Run 1: The Virtuous Mission |
| You Snooze, You Lose | Bronze | The trophy for getting behind The End unseen and holding him at gunpoint. | 6. Run 1: Svyatogornyj and Sokrovenno |
| Prince Charming | Bronze | Earned for shooting your first Kerotan. | 1. Run 1: The Virtuous Mission |
| Ralph Called | Bronze | Earned for making Snake throw up. | 2. Run 1: Dremuchij to Rassvet |
| Problem Solved, Series Over | Bronze | Earned for the time paradox: ending Ocelot during the Virtuous Mission gives a special game over screen. | 1. Run 1: The Virtuous Mission |
| The Cat's out of the Bag | Bronze | The trophy for the fifth hidden first-person view, in the scene in the hall near the end. | 10. Run 1: The Hangar to Rokovoj Bereg |
| Snake Eyes | Bronze | The trophy for all six hidden first-person views, taken in this run. | 10. Run 1: The Hangar to Rokovoj Bereg |
| Just What the Doctor Ordered | Bronze | The trophy for holding every medicinal plant: the Amur Kudzu, the Ezo Comfrey, the Chinese Plantain and the Slav Horehound. | 6. Run 1: Svyatogornyj and Sokrovenno |
| Everything Is in Season | Bronze | Earned for having all three fruit types: the Russian False Mango, the Golova and the Yabloko Moloko. | 1. Run 1: The Virtuous Mission |
| Fungus Among Us | Bronze | The trophy for holding every mushroom type, A to G. | 6. Run 1: Svyatogornyj and Sokrovenno |
| A Bird in the Hand... | Bronze | The trophy for holding every bird type: the Sunda Whistling-Thrush, the Magpie, the Red Avadavat, the Parrot and the White-Rumped Vulture. | 7. Run 1: Krasnogorje and the Underground Tunnel |
| Charmer | Bronze | The trophy for holding every snake type, SNAKE A to SNAKE K. | 10. Run 1: The Hangar to Rokovoj Bereg |
| Tall Tale | Bronze | The trophy for holding every fish type: the Arowana, the Maroon Shark and the Bigeye Trevally. | 5. Run 1: Ponizovje and Graniny Gorki |
| Them's Good Eatin' | Bronze | The trophy for holding all three frog types, taken in this run: the Tree Frog, the Otton Frog and the Poison Dart Frog. | 3. Run 1: Chyornyj Prud and Bolshaya Past |
| With All Guns Blazing | Bronze | The trophy for holding every type of weapon. | 9. Run 1: Groznyj Grad Sewers to Tikhogornyj |
| Cover-to-Cover Solid 3: Book Eater | Bronze | The only trophy earned outside the game itself: read the whole Screenplay Book in the Master Collection launcher. | 13. Screenplay Book, Demo Theater and Special |
| Believe It or Not | Silver | The trophy for catching a Tsuchinoko. | 3. Run 1: Chyornyj Prud and Bolshaya Past |
| The Early End | Silver | Shoot The End at the docks, long before his own fight, for this trophy. | 5. Run 1: Ponizovje and Graniny Gorki |
| It Ain't Easy Being Green | Silver | The trophy for shooting all 64 Kerotans, taken in this run. | 10. Run 1: The Hangar to Rokovoj Bereg |
| Fashionista | Silver | The trophy for every type of camouflage. | 11. Run 1: The Results Screen |
| Only Skin Deep | Silver | The trophy for every type of face paint: the six found in run 1 and the Infinity Face Paint. | 11. Run 1: The Results Screen |
| King of the Jungle | Silver | The trophy for the MARKHOR codename: every one of the 48 plant and animal types held at least once in one run. | 11. Run 1: The Results Screen |
| Under the Radar | Silver | Stealth (Under the Radar) | 11. Run 1: The Results Screen |
| Fit For a King | Silver | Face Paint: Infinity | 11. Run 1: The Results Screen |
| PEACE WALKER | Silver | The trophy for finishing a run without killing anyone. | 11. Run 1: The Results Screen |
| The Coast Is Clear | Gold | The trophy for finishing a run without ever entering an alert phase. | 11. Run 1: The Results Screen |
| FOXHOUND | Gold | The title for a clean Extreme run inside every limit in the run 2 limits table. | 12. Run 2: Extreme, the FOXHOUND Run |