The selection of enzyme blend is critical for the success of human islet isolations. Liberase HI collagenase (Roche) was introduced in the 1990s and had been widely used for clinical islet transplantation. More recently, a blend collagenase NB1 has been rendered available. The aim of this study was to evaluate the isolation outcomes and islet quality comparing human islet cells processed using NB1 and Liberase HI. A total of 90 isolations processed using NB1 (n = 40) or Liberase HI (n = 50) was retrospectively analyzed. Islet yield, function in vitro and in vivo, cellular (including β-cell-specific) viability and content, as well as isolation-related factors were compared. No significant differences in donor-related factors were found between the groups. There were also no significant differences in islet yields (NB1 vs. Liberase: 263,389 ± 21,550 vs. 324,256 ± 27,192 IEQ; p = n.s., respectively). The pancreata processed with NB1 showed a significantly longer digestion time (18.6 ± 0.7 vs. 14.5 ± 0.5 min, p < 0.01), lower β-cell viability (54.3 ± 3.4% vs. 72.0 ± 2.1%, p < 0.01), β-cell mass (93,671 ± 11,150 vs. 148,961 ± 12,812 IEQ, p < 0.01), and viable β-cell mass (47,317 ± 6,486 vs. 106,631 ± 10,228 VβIEQ, p < 0.01) than Liberase HI. In addition, islets obtained with Liberase showed significantly better graft function in in vivo assessment of islet potency. The utilization of collagenase NB1 in human islet isolation was associated with significantly lower β-cell viability, mass, and islet potency in vivo in our series when compared to Liberase HI, even though there was no significant difference in islet yields between the groups. Evaluation of viable β-cell mass contained in human islet preparations will be useful for selecting enzyme blends.