An inverse association has been reported between coffee drinking and the risk of hepatocellular carcinoma (HCC) and chronic liver disease (CLD), but its magnitude is still unclear. Thus, we carried out a systematic review and meta-analysis of prospective cohort studies that investigated the association between coffee consumption and the risk of HCC or CLD. We separately estimated the relative risk (RR) of the two conditions, for regular, low, and high consumption compared with no or occasional coffee consumption; we also calculated the summary RR for an increment of one cup of coffee per day. Twelve studies on HCC (3414 cases) and six studies on CLD (1463 cases) were identified. The summary RRs for HCC were 0.66 [95% confidence interval (CI): 0.55–0.78] for regular, 0.78 (95% CI: 0.66–0.91) for low, and 0.50 (95% CI: 0.43–0.58) for high coffee consumption, respectively. The summary RR for an increment of one cup per day was 0.85 (95% CI: 0.81–0.90). The summary RRs for CLD were 0.62 (95% CI: 0.47–0.82) for regular, 0.72 (95% CI: 0.59–0.88) for low, 0.35 (95% CI: 0.22–0.56) for high, and 0.74 (95% CI: 0.65–0.83) for an increment of one cup per day. The present meta-analysis provides a precise quantification of the inverse relation between coffee consumption and the risk of HCC, and adds evidence to the presence of an even stronger negative association with CLD.