In recent experiments involving metal-assisted secondary ion mass spectrometry (MetA-SIMS), either an increase or a decrease of the sputtered organic ion yield was demonstrated depending whether the incoming projectile was atomic (Ga, In) or polyatomic (Bi 3 , C 60 ). Theoretically, the electronic and molecular processes governing the yield variation are still poorly understood for metal-organic surfaces. To unravel the physics of sputtering, molecular dynamics simulations involving metal-organic samples have been implemented. Two targets mimicking, respectively, a gold/organic vertical interface and a molecular sample covered by gold nanoparticles were designed and bombarded with several projectiles, including Ga and C 60 . The results emphasize the differences of emission and molecular mechanisms induced by these projectiles and explain some of the effects observed in MetA-SIMS.