Asylum recognition rates in advanced democracies differ not only across states but also vary within them, translating into fluctuating individual chances to obtain protection. Existing studies on the determinants of these regional inequities typically rely on aggregate data. Utilizing a German refugee survey and leveraging a quasi-natural experiment arising from state-based allocation rules tied to national dispersal policies, we test two explanations for the perplexing regional differences. Drawing on principal–agent models of administrative decision-making, we test whether asylum decision-makers consciously or unconsciously comply with regional political preferences between 2015 and 2017 in Germany, one of the major European destination countries for refugee migration. We furthermore explore whether such biased decision-making amplifies in times of organizational stress as suggested by the statistical discrimination theory. Using mixed-effects logistic regressions, our analyses confirm a lower approval probability in regions with more immigration-averse residents or governments. We cannot confirm, however, that this association is mediated by high workloads or large knowledge gaps. Our results thus suggest that regional political biases affect the individual chance of asylum-seekers to obtain protection irrespective of temporal administrative conditions.