Internet-delivered transdiagnostic anxiety interventions aim to reduce symptoms across several anxiety disorders using one treatment protocol. However, it is unclear whether comorbidity affects outcomes of such treatment. This study re-examined data from a recent randomised controlled trial (N = 129) that evaluated the efficacy of an Internet-delivered transdiagnostic cognitive behavioural therapy (iCBT) intervention for participants with principal diagnoses of generalised anxiety disorder (GAD), social phobia (SP) panic disorder and agoraphobia (PDA), of whom 72% met criteria for a comorbid anxiety disorder or depression. Participants were divided into two groups based on whether or not they had a comorbid disorder before treatment. Participants with comorbid conditions reported higher symptom levels at pre-treatment, post-treatment, and follow-up across a range of measures. Both groups showed significant reductions in symptoms over treatment; however, participants with comorbid disorders showed greater reductions in measures of GAD, PDA, SP, depression, and neuroticism. In addition, treatment significantly reduced the number of comorbid diagnoses at follow-up. These results indicate transdiagnostic iCBT protocols have the potential to reduce comorbidity.