Recent years were characterized by meaningful chances in the working conditions for many employees. Specifically, access to flexibility reached a new high during the COVID-19 pandemic, spurring research endeavors on the consequences of these changes. This study contributes to these efforts by exploring the effects of reactive and proactive workplace flexibility on perceived overall justice in employees with and without disabilities. Building on the Conservation of Resources (COR) theory, we hypothesized that access to flexibility increased employees’ perceived justice over time and expected a more pronounced positive effect for employees with disabilities. We tested these hypotheses in a representative sample of N = 3695 employees in Germany, including N = 488 employees with disabilities and N = 3207 employees without disabilities. We could investigate the within-person effect over time by utilizing longitudinal data collected at three measurements over one year and employing random-intercept cross-lagged panel models (RI-CLPM). According to our results, no significant effect of reactive workplace flexibility on perceived justice was found in either group. While employees without disabilities also showed no effect of proactive workplace flexibility on perceived overall justice, a positive effect of proactive workplace flexibility in employees with disabilities emerged. Our findings show a nuanced picture of the effects of different types of workplace flexibility, providing important theoretical and practical implications.