There is scarce and conflicting evidence on the comparison between endoscopic ultrasound (EUS) and percutaneous (PC)-guided liver biopsy (LB). The aim of this study was to compare the two approaches in a series of patients with parenchymal and focal liver lesions. Fifty-four patients undergoing EUS-LB in two high-volume centers between 2017 and 2021 were compared to 62 patients who underwent PC-LB. The primary outcome was diagnostic adequacy rate. The secondary outcomes were diagnostic accuracy, total sample length (TSL), number of complete portal tracts (CPTs), procedural duration, and adverse events. Variables were compared using the Chi-square and Mann–Whitney test. Median age was 56 years (interquartile range 48–69) in the EUS-LB group and 54 years (45–67) in the PC-LB group with most patients being male. Indication for LB was due to parenchymal disease in 50% of patients, whereas the other patients underwent LB due to focal liver lesions. Diagnostic adequacy was 100% in PC-LB and 94.4% in the EUS-LB group (p = 0.74), whereas diagnostic accuracy was 88.8% in the EUS-LB group and 100% in the PC-LB group (p = 0.82). Median TSL was significantly greater in the PC-LB group (27.4 mm, IQR 21–29) when compared to the EUS-LB group (18.5 mm, 10.1–22.4; p = 0.02). The number of complete portal tracts was 21 (11–24) in the PC-LB group and 18.5 (10–23.2) in EUS-LB group (p = 0.09). EUS-LB was a significantly longer procedure (7 min, 5–11 versus 1 min, 1–3 of PC-LB; p < 0.001) and no evidence of adverse events was observed in any of the study groups. These results were confirmed in the subgroup analysis performed according to an indication for LB (parenchymal disease versus focal lesion). Although PC-LB yielded specimens with greater TSL, diagnostic adequacy and accuracy were similar between the two procedures.