Introduction Shift work has been associated with cardiometabolic risk factors, but the relation is not clear for all risk factors, and the role of chronotype is largely unknown. We examined associations between shift work and cardiometabolic risk factors, and explored these associations in different chronotypes. Methods Risk factors (anthropometry, blood pressure, lipids, glucose, gamma-glutamyltransferase, C-reactive protein, uric acid, and glomerular filtration rate) were assessed among 7768 adults in 1987–1991, with repeated measurements every five years. In the ongoing 6th examination wave data on shift work history have been collected, with data from 2013–2015 being available. In 2016, linear mixed models and logistic generalised estimating equations were used to estimate associations between shift work and risk factors one year later. Results Shift workers had more often overweight (OR: 1.44, 95% CI: 1.06–1.95) and a higher body mass index (BMI) (β: 0.56 kg/m2, 95% CI: 0.10–1.03) than day workers. A significant difference in BMI between day and shift workers was observed among evening chronotypes (β: 0.97 kg/m2, 95% CI: 0.21–1.73), but not among morning chronotypes (β: 0.04 kg/m2, 95% CI: −0.85–0.93). No other significant associations between shift work and risk factors were found in the chronotype strata, except for glucose among intermediate chronotypes (β: −0.36, 95% CI: −0.62–0.11). No differences by frequency of night shifts and duration of shift work were observed. Conclusions Shift workers, in particular evening chronotypes, have a higher risk of overweight than day workers. More research is however needed to verify our results, and establish whether tailored interventions by chronotype are wanted.