Abstract Background Anxiety-, mood/affective-, or stress-related disorders affect up to one-third of individuals during their lives and often impact their ability to work. This study aimed to delineate trajectories of work disability (WD) among individuals diagnosed with anxiety-, mood/affective-, or stress-related disorder in primary healthcare and to examine associations between trajectory group membership and sociodemographic, clinical, and clinical-related factors. Methods The study population included working-age individuals, aged 22–62 years, living in Stockholm County, Sweden, who experienced a new episode of any anxiety-, mood/affective, or stress-related disorder in primary healthcare in 2017 (N = 11,304). Data were obtained from Swedish national and regional registers and were linked using pseudonymised unique personal identification numbers. The primary outcome was days with WD (sum of sickness absence and disability pension days) during the three years before and three years after a diagnosis of anxiety-, mood/affective-, or stress-related disorders in primary healthcare. A zero-inflated Poisson group-based trajectory model was used to identify groups of individuals with similar patterns of WD over the study period, with a multinomial logistic regression used to examine associations of sociodemographic, clinical, and clinical-related factors with trajectory group membership. Results Four distinct trajectory groups were found, high increasing (5.1%), with high levels, from 16 to 80 days of WD in six-monthly intervals during follow-up, peak (11.1%), with a peak in WD, up to 32 days of WD, around the time of the diagnosis, low increasing (12.8%), with an increase in days of WD from 4 to 22 during the study period, and constant low (71.1%), with almost no WD over the study period. In multinomial regression models, diagnostic category, psychotropic medication use, a diagnosis of a psychiatric disorder within secondary healthcare, age at diagnosis, and occupation were associated with WD trajectory groups. Conclusions Around two-thirds of individuals treated for a new episode of any anxiety-, mood/affective-, or stress-related disorder in primary healthcare have an excellent prognosis regarding WD. Several sociodemographic and clinical characteristics were associated with group membership; these factors could identify individuals at risk of long-term welfare dependency and who might benefit from interventions to promote a return to work.