More than half of patients with colorectal cancer develop liver metastases during the course of their disease, at which point their survival outlook is usually very poor. A significant proportion of patients receive neoadjuvant FOLFOX (5-Fluorouracil, Oxaliplatin, Leucovorin) prior to surgery to enable successful surgical removal of metastases or reduce the risk of recurrence. Yet, most of these patients progress during treatment or recur following surgery, and molecular mechanisms that contribute to FOLFOX resistance remain poorly understood. Here we sought to characterize these mechanisms using a combination of genomic, transcriptomic and phenotypic analyses of tumor samples and matching organoids collected from patients with metastatic CRC. Chemo-resistant organoids, identified after in vitro exposure to FOLFOX, were characterized by elevated expression of genes involved in the E2F pathway and in the TP53 independent G1/S, G2/M and spindle assembly checkpoints (SAC). Liver metastases from patients with progressive disease while under neoadjuvant FOLFOX chemotherapy demonstrated similar molecular features, highlighting the clinical relevance of this finding. Using flow cytometry and immunostaining, we show that FOLFOX resistant organoids accumulate undergo a G1/S cell cycle arrest and sustain significant DNA damage during FOLFOX exposure, then accumulate in G2/M without dividing while repairing their DNA during the first few days following FOLFOX removal. In parallel, results of a large, unsupervised kinase inhibitor screen indicate that drugs targeting regulators of the G1/S and G2M checkpoint had strong cytotoxic effects on organoids derived from patients whose disease progressed under FOLFOX treatment. Further validation experiments demonstrated that concomitant exposure to CHK1 or Wee1 inhibitors was very effective to re-sensitize FOLFOX-resistant organoids. In addition, inhibiting the SAC master regulator MPS1/TTK was very effective to induce cell death in FOLFOX-resistant organoids when used immediately after FOLFOX, while cells are accumulating in G2M. Our results suggest that targeting the DNA damage induced, TP53 independent G1/S or G2M cell cycle checkpoints may significantly improve response rates to FOLFOX in patients with metastatic colorectal cancer.