Purpose Research shows that psychosocial factors play a significant role in the emergence of musculoskeletal complaints (MSC). The aim of this study was to determine the long-term effects on unspecific MSC by a combined physiotherapy and coaching intervention compared to physiotherapy alone. The coaching intervention focussed on enabling better strategies for coping with work stressors. Methods The participants of a previous randomized controlled intervention were invited to participate again in a third follow-up survey 22 months after the end of the intervention. In 2014, 65 nurses completed a 10-week personalised physiotherapy. Additionally, the intervention group ( n = 33) passed five individual coaching sessions, plus an opening and closing session. 44 nurses (IG: n = 24; CG: n = 20) passed again a physical examination as well as another questionnaire assessment in 2016. The primary outcome was MSC, secondary outcomes were work ability and work-related well-being. Due to missing data, multiple imputations were conducted using the mice package in R. Data were analysed by ANOVA with two-way repeated measures, t tests for independent samples and Chi-squared tests. Results In respect of MSC, stronger improvement of movement in the vertebral column was observed in the IG compared to the CG. No differences between the IG and CG regarding other long-term effects were observed. Conclusions The results suggest that the combined intervention of work-related coaching and physiotherapy had only a marginally stronger long-term effect with respect to MSC than physiotherapy alone.