Work-related sickness absence carries large societal costs, and interventions aimed at decreasing sickness absence need to be performed in an effective way. This study evaluated the implementation process of an operational-level job stress intervention, implemented between 2017 and 2018 in the public sector, by assessing the extent to which the allocated resources reached the intended target group, if the planned measures could be expected to address the relevant work environmental challenges, and if the planned measures were implemented. Data were collected from applications for funding in the intervention (n = 154), structured interviews (n = 20), and register data on sickness absence (n = 2912) and working conditions (n = 1477). Thematic analysis was used to classify the level of the work environmental challenges, the level and perspective of the suggested measures, and the “measure-to-challenge correspondence”. Overall, participating workplaces (n = 71) had both higher sickness absence (p = 0.01) and worse reported working conditions compared to their corresponding reference groups. A measure-to-challenge correspondence was seen in 42% of the measures, and individual-level measures were mostly suggested for organisational-level work environment challenges. Almost all planned measures (94%) were ultimately implemented. When performing operational-level interventions, managers and their human resource partners need support in designing measures that address the work environmental challenges at their workplace.