Background <p>This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.</p> Methods <p>The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (<i>n</i> = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (<i>n</i> = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.</p> Results <p>Durable disease control (PFS ≥ 24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the <i>SP140</i> transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of <i>Prevotella</i> was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.</p> Conclusions <p>ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by <i>Prevotella</i> abundance, and can induce durable disease control in a subgroup of patients.</p> Trial Registration <p>ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).</p>