Today’s companies are complex, interconnected entities that coordinate resources and processes across multiple decision-making levels. This coordination, traditionally led by humans, spans various scales—from workstations to entire production sites—adding layers of complexity. To address this, the paper introduces a framework for designing a decision-support system aligned with human cognitive functioning, considering multi-level and multi-scale settings. The framework aims to manage the company’s multilayered characteristics while ensuring coherence in decision-making. Specifically, it seeks to: (1) support adaptable organizational decision-making; (2) provide insights into the impact of decisions at different levels; and (3) explore the synergy between human expertise and automation. The paper concludes with a case study demonstrating the framework’s importance and proposes a solution for future validation.