Purpose The study aim was to compare the disease control in two groups of patients affected by liver metastases from CRC treated with microwave ablation (MWA) or stereotactic body radiation therapy (SBRT). Methods We extracted data of patients treated between 2009 and 2016. Inclusion criteria were: (1) maximum diameter of the liver lesions less than 4 cm; (2) no more than three liver lesions; (3) no evidence of progressive or untreated gross disease outside the liver; (4) adequate liver function; (5) no concurrent chemotherapy; (6) minimum age of 18. Tumour response was classified according to EORTC-RECIST criteria. Aim of the present study was to evaluate freedom from local progression (FFLP). To reduce indication bias, an inverse probability of treatment weighting was used to estimate treatment effect. Results A total of 135 patients with 214 lesions were included in the analysis. Median follow-up time was 24.5 months (range 2.4–95.8). The 1-year freedom from local progression (FFLP) was 88% (95%CI 80–92). In the SBRT group, FFLP was statistically longer than MWA group ( p  = 0.0214); the 1-year FFLP was 91% (95% CI 81–95) in SBRT group and 84% (95% CI 0.72–0.91) in MWA group. Patients treated with SBRT showed a reduce risk of local relapse compared to MWA (adjusted HR 0.31; 95%CI 0.13–0.70, p  = 0.005). As expected, analogous result obtained in the inverse probability weighting analysis (HR 0.38; 95%CI 0.18–0.80; p  = 0.011). Conclusion In conclusion, there seems to be an advantage of SBRT compared to MWA in treating CRC liver metastases, particularly for lesions bigger than 30 mm