The in-depth assessment of work-related stress risk (WRS) represents both a regulatory obligation and a moment to reflect on the health conditions of the organization. This paper reports the results obtained from the in-depth WRS assessment conducted in a facility management company through the administration of the HSE Management Standards Indicator Tool (HSE-MS IT) and further measures aimed at assessing perceived stress, job satisfaction, and job motivation. A total of 196 workers took part in the study. The WRS assessment revealed the presence of risk in the Demand, Relationships, and Peer Support dimensions and of serious risk in the Control dimension. Through correlations and multiple regressions analyses the organizational areas significantly associated with perceived stress, job satisfaction and job motivation have been identified. The direct and indirect effect of the Management Standards on the three output measures was also evaluated using path analysis models. Demand, Control, and Relationships resulted to have a direct effect on perceived stress, while Peer Support and Management Support had an effect on job satisfaction and job motivation respectively. Perceived stress also has a direct effect on job satisfaction, which in turn resulted to affect job motivation. In conclusion, an in-depth WRS assessment that combines the traditional approach based on Management Standards with additional measures of organizational well-being, can give the opportunity to identify not only the key factors leading to WRS, but also the management areas critically associated to other elements that contribute to organizational well-being, such as job satisfaction and motivation.