5-fluorouracil (5-FU) is the backbone for chemotherapy in colorectal cancer (CRC), however response rates in patients are limited to 50%. Unexpectedly, the molecular mechanisms by which 5-FU ultimately induces toxicity remain debated, limiting the development of strategies to improve its efficacy. How fundamental aspects of cancer, such as driver mutations and phenotypic intra-tumor heterogeneity, relate to the 5-FU response are ill-defined. This is largely due to a shortage of mechanistic studies in pre-clinical models able to recapitulate the key-features of CRC. Here, we analyzed the 5-FU response in human organoids genetically engineered to reproduce the different stages of CRC progression. We find that 5-FU induces pyrimidine imbalance, which leads to DNA damage and cell death. Actively proliferating cancer (stem) cells are, accordingly, efficiently targeted by 5-FU. Importantly, p53 behaves as a discriminating factor for 5-FU sensitivity, whereas p53-deficiency leads to DNA damage-induced cell death, active p53 protects from these effects through inducing cell cycle arrest. Moreover, we find that targeting the Warburg effect, by rewiring glucose metabolism, enhances 5-FU toxicity by altering the nucleotide pool and without increasing toxicity in non-transformed cells. Thus, rewiring glucose metabolism in combination with replication stress-inducing chemotherapies emerges as a promising strategy for CRC treatment.