Abstract Robustness is pervasive throughout biological systems, enabling them to maintain persistent outputs despite perturbations in their components. Here, we reveal a mechanism contributing to leaf morphology robustness in the face of genetic perturbations. In Arabidopsis (Arabidopsis thaliana), leaf shape is established during early development through the quantitative action of the CUP-SHAPED COTYLEDON2 (CUC2) protein, whose encoding gene is negatively regulated by the co-expressed MICRORNA164A (MIR164A) gene. Compromised epigenetic regulation due to defective Polycomb Repressive Complex 2 (PRC2) function results in the transcriptional derepression of CUC2 but has no impact on CUC2 protein dynamics or early morphogenesis. We solve this apparent paradox by showing that compromised PRC2 function simultaneously derepresses the expression of another member of the MIR164 gene family, MIR164B. This mechanism dampens CUC2 protein levels, thereby compensating for compromised PRC2 function and canalizing early leaf morphogenesis. Furthermore, we show that this compensation mechanism is active under different environmental conditions. Our findings shed light on how the interplay between different steps of gene expression regulation can contribute to developmental robustness.