Many companies, despite there being opportunities for automation in production and logistics (P&L) systems, still rely on human workers due to their cognitive and motor skills. Taking Human Factor (HF) aspects into consideration when making P&L system design and management decisions is therefore important, an ignorance of HF potentially resulting in operator fatigue, discomfort, subsequent injuries and negative consequences for operator performance and the P&L system. A review of the literature shows that the majority of studies that take HF into consideration focus either on designing the workplace or on operation planning activities. There is also still a gap in the literature. Little has been published on P&L systems that incorporate HF and that combine different levels of shortterm operational policy decisions (e.g. job allocation) and long-term system characteristic decisions (e.g. layout design). Current state-of-the-art frameworks that support the design and management of P&L systems and that take HF into consideration rarely consider different decision levels. This study proposes a new framework that incorporates HF into P&L systems by combining different levels of decisions to improve performance, quality, and well-being.