Objectives Lower limb tendinopathy (LLT) is highly prevalent in runners. Treatment can be challenging, and knowledge of risk factors may be valuable to develop preventive or treatment interventions for LLT. The aims of this study were (1) to assess the prevalence of three common LLTs (Achilles tendinopathy (AT), patellar tendinopathy and plantar fasciopathy) in a large cohort of Dutch and Belgian runners and (2) to investigate its association with potential risk factors, with a particular focus on nutritional factors in the habitual diet. Methods A total of 1993 runners were included in the study. They completed two online questionnaires: a general questionnaire on running habits and injuries and a Food Frequency Questionnaire. Runners with and without LLT were compared regarding personal characteristics, running characteristics and nutritional factors. Results The point prevalence for the three LLTs was 6%; 33% of the runners reported LLT in the past and 35% had either a current or past LLT. AT was the most prevalent type of LLT, and prevalence rates for all types of LLT were higher in men than women. Positive associations with LLT were observed for age and running years (men and women), running level and running distance (men). No associations between LLT and nutritional factors were observed. Conclusion One-third of this population of runners had ever experienced an LLT. These tendinopathies were associated with gender, age and running load, but not with nutritional factors.