Abstract Objectives The incidence of running-related injuries is high. Some risk factors for injury were identified in novice runners, however, not much is known about the effect of training factors on injury risk. Therefore, the purpose of this study was to examine the associations between training factors and running-related injuries in novice runners, taking the time varying nature of these training-related factors into account. Design Prospective cohort study. Methods 1696 participants completed weekly diaries on running exposure and injuries during a 6-week running program for novice runners. Total running volume (min), frequency and mean intensity (Rate of Perceived Exertion) were calculated for the seven days prior to each training session. The association of these time-varying variables with injury was determined in an extended Cox regression analysis. Results The results of the multivariable analysis showed that running with a higher intensity in the previous week was associated with a higher injury risk. Running frequency was not significantly associated with injury, however a trend towards running three times per week being more hazardous than two times could be observed. Finally, lower running volume was associated with a higher risk of sustaining an injury. Conclusions These results suggest that running more than 60 min at a lower intensity is least injurious. This finding is contrary to our expectations and is presumably the result of other factors. Therefore, the findings should not be used plainly as a guideline for novices. More research is needed to establish the person-specific training patterns that are associated with injury.