This article investigates the influence of the organic film thickness on the characteristic and molecular ion yields of polystyrene (PS), in combination with two different substrates (Si, Au) or gold condensation (MetA-SIMS), and for atomic (Ga+) and polyatomic (C60+) projectile bombardment. PS oligomer (m/z approximately 2000 Da) layers were prepared with various thicknesses ranging from 1 up to 45 nm on both substrates. Pristine samples on Si were also metallized by evaporating gold with three different thicknesses (0.5, 2, and 6 nm). Secondary ion mass spectrometry was performed using 12 keV atomic Ga+ and C60+ projectiles. The results show that upon Ga+ bombardment, the yield of the fingerprint fragment C7H7+ increases as the PS coverage increases and reaches its maximum for a thickness that corresponds to a complete monolayer (approximately 3.5 nm). Beyond the maximum, the yields decrease strongly and become constant for layers thicker than 12 nm. In contrast, upon C60+ bombardment, the C7H7+ yields increase up to the monolayer coverage and they remain constant for higher thicknesses. A strong yield enhancement is confirmed upon Ga+ analysis of gold-metallized layers but yields decrease continuously with the gold coverage for C60+ bombardment. Upon Ga+ bombardment, the maximum PS fingerprint ion yields are obtained using a monolayer spin-coated on gold, whereas for C60+, the best results are obtained with at least one monolayer, irrespective of the substrate and without any other treatment. The different behaviors are tentatively explained by arguments involving the different energy deposition mechanisms of both projectiles.