Background Non-adherence in Internet interventions is a persistent and multifaceted issue and potentially limits the applicability and effectiveness of these interventions. Factors that influence non-adherence are poorly understood, especially in outpatient samples with more complex symptoms. Objective The current study is a secondary analysis of data from a randomised controlled trial that examined the cost-effectiveness of offering an Internet-based exposure treatment to phobic outpatients on a wait-list to receive face-to-face psychotherapy. Methods We collected baseline demographic and clinical information, and adherence data of the Internet-based intervention and conducted regression analyses to predict non-adherence to the intervention. Results The adherence to the intervention was low, with only 13.3% of 105 patients completing all five lessons of the intervention. The median number of exercises completed (out of a possible 8) was 3. In a multi-predictor model, a higher baseline score of anxiety (OR = 0.94, 95% CI 0.90–0.99) was a risk factor for low adherence. Higher age (OR = 1.05, 95% CI 1.00–1.09) was a protective factor against non-adherence. Participants who adhered to the intervention were more likely to complete post-test assessments, further biasing results. However, overall participant attrition was high. The results are based on a small subset of participants and should be interpreted with caution. Conclusions Poor baseline clinical status and age are factors to consider when deciding whether to offer an Internet-based intervention to outpatients. Low adherence among those patients might be related to intrinsic motivation and might even be lower in outpatient settings where participants expect to receive face-to-face treatment. It might be worthwhile to develop a concise instrument to assess intrinsic motivation and treatment expectations for using Internet-based interventions, and for the therapist to review the range of possible (Internet-based) intervention options to suit personal preferences and expectations. Trial registration Netherlands Trial Register, NTR2233.