It is expected that exposure to airborne microorganisms among waste recycling workers depends on type of plant (composting, biogas-producing, and sorting plant). Previous studies among waste recycling workers at selected plants indicated gastrointestinal symptoms related to bioaerosol exposure. This nationwide study reports findings of self-reported gastrointestinal symptoms by self-reported type of plant. A questionnaire based survey among Danish waste recycling workers (n = 432) at all composting, biogas-producing, and sorting plants collected data on occupational exposures, present and past work environment, the psychosocial work environment, and health status. Two hundred and seventy-seven participated and the response rate was 64%. Prevalence Proportion Ratios (PPR) adjusted for other possible types of job and relevant confounders were estimated by multivariate logistic regression with a comparison group of non-exposed workers. Sorting of paper was associated with reports of diarrhoea. Working with sorting of plastic was associated with nausea, and working with compost was associated with diarrhoea. Females reported more symptoms than males. This study confirmed the association between gastrointestinal symptoms and the type of recycling plant.