Audit data is important in creating a clear picture of clinical reality in clinical services, and evaluating treatment outcomes. This paper explored the data from an audit of a large national eating disorder (ED) service and evaluated the outcome of inpatient and day treatment programmes for patients with anorexia nervosa (AN) with and without autistic traits. Four hundred and seventy-six patients receiving treatment for AN at inpatient (IP), day-care (DC) and step-up (SU) programmes were assessed at admission and at discharge on the following measures: autistic traits, body-mass-index (BMI), ED symptoms, depression and anxiety symptoms, work and social functioning, and motivation for change. Outcomes were analyzed first at a within-group level based on change in mean scores and then at an individual level based on the clinical significance of improvement in eating disorder symptoms. Outcomes were compared between patients with high autistic traits (HAT) and low autistic traits (LAT) in each programme. The findings suggest that 45.5% of DC and 35.1% of IP patients showed clinically significant changes in ED symptoms following treatment. Co-occurring high autistic traits positively predicted improvement in ED symptoms in IP setting, but was a negative predictor in DC. In IP, more HAT inpatients no longer met the BMI cut-off for AN compared to LAT peers. In terms of general psychopathology, patients with AN and HAT exhibited more severe depression symptoms, anxiety symptoms and social functioning impairment than their LAT peers, and these symptoms stayed clinically severe after treatment. Patients with AN and hight autistic traits are more likely than their peers with low autistic traits to show weight restoration and improvement in ED systems after inpatient treatment. This reverses in DC, with high autistic trait patients less likely to improve after treatment compared to low autistic trait patients. Our results suggest that inpatient treatment with individualized and structured routine care may be an effective model of treatment for patients with AN and high autistic traits.