The NOAA Warn-on-Forecast System (WoFS) is an experimental rapidly updating convection-allowing ensemble designed to provide probabilistic operational guidance on high-impact thunderstorm hazards. The current WoFS uses physics diversity to help maintain ensemble spread. We assess the systematic impacts of the three WoFS PBL schemes—YSU, MYJ, and MYNN—using novel, object-based methods tailored to thunderstorms. Very short forecast lead times of 0–3 h are examined, which limits phase errors and thereby facilitates comparisons of observed and model storms that occurred in the same area at the same time. This evaluation framework facilitates assessment of systematic PBL scheme impacts on storms and storm environments. Forecasts using all three PBL schemes exhibit overly narrow ranges of surface temperature, dewpoint, and wind speed. The surface biases do not generally decrease at later forecast initialization times, indicating that systematic PBL scheme errors are not well mitigated by data assimilation. The YSU scheme exhibits the least bias of the three in surface temperature and moisture and in many sounding-derived convective variables. Interscheme environmental differences are similar both near and far from storms and qualitatively resemble the differences analyzed in previous studies. The YSU environments exhibit stronger mixing, as expected of nonlocal PBL schemes; are slightly less favorable for storm intensification; and produce correspondingly weaker storms than the MYJ and MYNN environments. On the other hand, systematic interscheme differences in storm morphology and storm location forecast skill are negligible. Overall, the results suggest that calibrating forecasts to correct for systematic differences between PBL schemes may modestly improve WoFS and other convection-allowing ensemble guidance at short lead times.