Introduction Sexual harassment (SH) at work can have an impact on the general health and well-being and on the productivity of the employee. To date, the Belgian Armed Forces do not have any accurate data about SH. Therefore, this study assessed the prevalence of SH within Belgian Defence. Methods The prevalence of SH and staff mental well-being was investigated in a sample of 399 female soldiers. Using quantitative analysis, we measured the impact on mental well-being and the relation to demographic characteristics. Using a qualitative analysis in a subsample of eight female soldiers, we investigated barriers to reporting SH and the impact on professional performance and psychosocial well-being. Results The prevalence of non-physical SH is 36.1% over the last 12 months and 64.4% over the course of a career. Physical SH has a prevalence of 16.1% and 43.4%, respectively. Rape prevalence was reported to be 1.4% over the past 12 months, 9% over the course of their career. One in three female soldiers suffer from reduced mental well-being, which was significantly associated with SH. In the interviews, female employees report an impact of SH on professional and personal performance. The willingness to report is low due to misunderstanding, disinformation and psychosocial insecurity. Conclusion High prevalence numbers were found suggesting an important impact on the professional performance and mental well-being of female military personnel. Organisational changes may create more willingness among victims to report incidents to the designated services.