The institutionalization of hybrid work arrangements has fundamentally reshaped the architecture of contemporary organizations, creating both significant opportunities and complex tensions in the management of human resources. Hybrid work models enhance employee autonomy by providing flexibility in terms of time, location, and task execution, thereby fostering greater control over work–life integration and supporting intrinsic motivation. However, this increased autonomy simultaneously necessitates the development of robust accountability mechanisms to ensure performance, coordination, and organizational alignment. This coexistence gives rise to a paradoxical dynamic in which autonomy, traditionally viewed as a key driver of well-being and engagement, intersects with accountability pressures that may lead to heightened stress, perceptions of surveillance, and psychological strain. This paper develops a comprehensive theoretical framework to examine this “Hybrid Work Paradox” by integrating insights from the Job Demands–Resources (JD-R) model, Self-Determination Theory (SDT), and social exchange perspectives. Within this framework, autonomy is conceptualized as a critical job resource that enhances motivation and well-being, while accountability is framed as a context-dependent job demand that can function as both enabling and constraining. The paper advances a series of theoretically grounded propositions, arguing that the positive effects of autonomy are contingent upon the design, intensity, and perceived fairness of accountability mechanisms. By articulating this nuanced interplay, the study contributes to organizational theory and offers a foundation for future empirical research and practical interventions in hybrid work contexts.