Social anxiety disorder (SAD) is a common mental disorder with high persistence when untreated. As access to effective treatment is limited, guided internet-based cognitive behavioral therapy (ICBT) has been proposed as an effective alternative to face-to-face treatment. In this study, we examined the effectiveness of a 14-week therapist-guided ICBT program for patients with SAD undergoing routine care. From 2014 to 2017, 169 patients were included in the study, of which 145 started the treatment. The sample was all general practitioner-referred and had a lower educational level and higher rate of work absence compared to similar effectiveness studies. Regarding social anxiety symptoms, we identified significant within-group effect sizes (post-treatment: d = 1.00–1.10; six-month follow-up: d = 1.03–1.55). We also found significant effects on secondary depression symptoms (d = 0.67). Clinically significant improvement was reported by 66.2% of the participants, and 16.6% had a significant deterioration. Clinical implications of the current study are that guided ICBT for SAD is an effective treatment for the majority of the patients undergoing routine care. Future studies should explore interventions targeting non-responders and deteriorated patients.