Background Symptoms of borderline personality disorder (BPD) were previously found to be associated with decreased work performance, even after controlling for depressive and anxiety disorders. Furthermore, co-occurrence of BPD and affective disorders is common. Therefore, we examined the effect of BPD symptoms on occupational functioning in workers with affective disorders. Methods Healthy workers (n = 287), workers with current depression/anxiety only (n = 195), workers with BPD symptoms only (n = 54), and workers with both depression/anxiety and BPD symptoms (n = 103) were selected from the Netherlands Study of Depression and Anxiety (NESDA). Both a categorical and dimensional approach were used to cross-sectionally study the effect of BPD symptoms on work performance and absenteeism. Results Compared to healthy controls, all symptomatic groups had impaired occupational functioning. Workers with current depression/anxiety had higher long-term absenteeism (OR = 3.59; 95%CI:1.83–7.02) and impaired work performance (OR = 7.81; 95%CI:4.44–13.73), workers with BPD symptoms only had higher impaired work performance (OR = 6.02 95%CI:2.76–13.09), and workers with both depression/anxiety and BPD symptoms had higher long-term absenteeism (OR = 3.66 95%CI:1.69–7.91) and impaired work performance (OR = 10.41 95%CI:5.38–20.15). No difference was found between the (symptomatic) groups. In the dimensional analysis, all associations between BPD symptoms and occupational measures disappeared when depressive symptoms were added. Depressive and BPD symptoms were highly correlated (r = .67). Conclusions Our findings confirm that both affective disorders and BPD symptoms are associated with occupational dysfunction. The effect of BPD symptoms however, seems mediated by depressive symptoms. This would suggest that focusing on affective symptoms in occupational health may be effective to improve occupational functioning in persons with BPD.