Ribosomes translating damaged mRNAs can stall, producing incomplete and potentially toxic polypeptides. These aberrant products are eliminated by the ribosome-associated quality control (RQC) pathway, a branch of the ubiquitin-proteasome system. RQC is triggered when stalled ribosomes collide with trailing ribosomes. The collided ribosomes are recognized by the E3 ligase Hel2 in yeast (ZNF598 in mammals), which ubiquitylates small ribosomal subunits. This modification leads to ribosome splitting, leaving incomplete nascent polypeptides attached to large subunits, where they are subsequently polyubiquitylated for proteasomal degradation. However, recent ribosome profiling studies have revealed widespread ribosome collisions across the transcriptome even under normal conditions, raising the question of whether such endogenous events are subjected to RQC. Collided ribosomes are also known to activate the integrated stress response (ISR), with Gcn1 acting as their sensor. In this study, we show that Gcn1 inhibits Hel2-dependent ribosome ubiquitylation and splitting, thereby protecting transiently collided ribosomes from premature RQC engagement. Thus, Gcn1 not only activates the ISR but also inhibits RQC. Although this regulatory mechanism operates under normal conditions, its effect is especially pronounced when amino acids are partially limiting, a condition that induces transient ribosome collisions. Overall, Gcn1 protects nascent polypeptides from unnecessary degradation by RQC.