Background: Workplace-related stress is a major risk factor for mental and physical health problems and related sickness absence and productivity loss. Despite evidence regarding the effectiveness of different workplace-based interventions, the implementation of stress prevention interventions is rare, especially in micro and small-sized enterprises (MSE) with fewer than 50 employees. The joint research project “PragmatiKK”⁺ aims to identify and address the specific barriers to the implementation of stress prevention interventions in MSE. This study protocol describes a mixed method study design to evaluate the effectiveness of adapted stress prevention interventions and the implementation process via an integrated web-based platform (“System P”) specifically targeted at MSE. Methods: First, we develop a web-based intervention, which accounts for the specific working conditions in MSE and addresses stress prevention at a structural and behavioral level. Second, we use common methods of implementation research to perform an effect and process evaluation. We analyze the effectiveness of the web-based stress prevention interventions by comparing depressive symptoms at baseline and follow-up (after 6 months and 12 months). Indicators for a successful implementation process include acceptability, adoption, feasibility, reach, dose, and fidelity, which we will measure with quantitative web-based questionnaires and qualitative interviews. We will also analyze the accumulated usage data from the web-based platform. Discussion: Collecting data on the implementation process and the effectiveness of a web-based intervention will help to identify and overcome common barriers to stress prevention in MSE. This can improve the mental health of employees in MSE, which constitute more than 90% of all enterprises in Germany. ⁺ Full Project Name: „PragmatiKK - Pragmatische Lösungen für die Implementation von Maßnahmen zur Stressprävention in Kleinst- und Kleinbetrieben “(= Pragmatic solutions for the implementation of stress prevention interventions in micro and small-sized enterprises). Trial registration: German Register of Clinical Studies (DRKS): DRKS00026154, date of registration: 2021-09-16.