In today’s rapidly evolving workplace, the imperative to study workers’ well-being has never been more apparent, considering both job-related risk factors and challenges posed by the digital transformation. Utilizing a large dataset from the recent European Working Conditions Telephone Survey (EWCTS) 2021, we explore the impact of physical and psychosocial risk factors on well-being and their interaction with the attributes of new forms of work brought by digitalization. Our methodological framework employs a suite of decision tree-based methods and sophisticated visual tools, designed to extract insights through a non-parametric approach. Findings reveal that increasing physical and emotional exhaustion and the need for recognition are predominant factors affecting employee well-being. Additionally, we find strong links between psychosocial risks, telework, and job locations.