The purpose of this pilot study was to examine the effectiveness of a 6-week workplace mindfulness- and self-compassion-based intervention (MSCBI) on perceived stress, burnout, immune functioning (assessed with the biomarker Immunoglobulin A), self-compassion, and experiential avoidance compared to a Workplace Stress Management Intervention. Both interventions were contextual, i.e., they were carried out in the workplace setting and during working hours. We followed a randomised controlled trial study design. The total sample was composed of 24 employees of an automotive company. One-way analyses of covariance between groups revealed significant differences in post-intervention levels of perceived stress, salivary Immunoglobulin A (sIgA), emotional exhaustion, self-compassion, and experiential avoidance, after adjusting for pre-test scores. The results of this study have several implications. Firstly, it confirms that MSCBIs might be more effective than regular psychoeducational interventions for work-related stress and burnout treatment. Secondly, sIgA can be used to assess immune function state changes when MSCBIs are carried out. Furthermore, these results indicate that it is feasible to carry out MSCBIs within companies and during working hours, and that these interventions can help effectively manage stress and burnout associated with the work environment.