In colorectal cancer (CRC), aberrant Wnt signalling is essential for tumorigenesis andmaintenance of cancer stem cells. However, how other oncogenic pathways converge onWnt signalling to modulate stem cell homeostasis in CRC currently remains poorly understood. Using large-scale compound screens in CRC, we identify MEK1/2 inhibitors as potentactivators of Wnt/β-catenin signalling. Targeting MEK increases Wnt activity in differentCRC cell lines and murine intestine in vivo. Truncating mutations of APC generated byCRISPR/Cas9 strongly synergize with MEK inhibitors in enhancing Wnt responses in isogenicCRC models. Mechanistically, we demonstrate that MEK inhibition induces a rapid downregulation of AXIN1. Using patient-derived CRC organoids, we show that MEK inhibition leadsto increased Wnt activity, elevatedLGR5levels and enrichment of gene signatures associatedwith stemness and cancer relapse. Our study demonstrates that clinically used MEK inhibitors inadvertently induce stem cell plasticity, revealing an unknown side effect of RASpathway inhibition.