This study assesses the potential of workplace-based micro-exercise (brief and simple exercise bouts) to prevent long-term sickness absence (LTSA) at the population level. In the Work Environment and Health in Denmark Study (2012-2018), we followed 70,130 workers from the general working population, without prior LTSA, for two years in the Danish Register for Evaluation of Marginalisation. We used Cox regression with model-assisted weights and controlled for various confounders. From 2012 to 2018, the percentage of workers in Denmark using workplace-based micro-exercise during and outside of working hours increased from 7.1 to 10.9% and from 0.8 to 1.4%, respectively. The incidence of long-term sickness absence (at least 30 days) was 8.4% during follow-up. The fully adjusted model showed reduced risk of long-term sickness absence from using micro-exercise during working hours, (HR 0.86, 95% CI 0.77-0.96), but not when used outside of working hours. If used by all workers, micro-exercise during working hours could potentially prevent 12.8% of incident long-term sickness absence cases (population attributable fraction). In conclusion, micro-exercise performed during working hours holds certain potential to prevent incident long-term sickness absence in the general working population. Large-scale implementation of workplace-based micro-exercise may represent an unexploited opportunity for public health promotion.