Abstract 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. Copyright © 2010 John Wiley & Sons, Ltd.