Background Most studies reporting treatment outcomes for eating disorders at higher levels of care focus on anorexia nervosa and bulimia nervosa. No studies have been published with a singular focus on examining treatment outcomes for adults receiving residential programming specifically designed for the treatment of binge eating spectrum disorders (BESD), including binge eating disorder and bulimia nervosa. Objective The purpose of this paper is to outline the protocol of a prospective study examining treatment outcomes at discharge and 3-month, 6-month, and 12-month postdischarge follow-up, for a sample of consecutive admissions to a residential program specifically for patients with BESD. Methods One hundred consecutive admissions to a binge eating treatment program were enrolled in the prospective single-arm trial between January 2019 and February 2020. Data were collected at admission, discharge, and 3, 6, and 12 months postdischarge, with admission, discharge, and 12-month follow-up as the major timepoints of interest. Results across the major timepoints will be analyzed with mixed effects general linear models. Results The primary aim is to assess the impact of the program on eating disordered behaviors at discharge and 12-month follow-up, which are hypothesized to improve as a result of treatment. Secondary hypotheses include improvements on comorbid symptoms, including trauma, depression, and obsessive-compulsive symptoms, as well as improvements on medical indicators of health, including cholesterol and triglycerides, at discharge and 12-month follow-up. Conclusions This study may aid in the development of treatment guidelines for patients with BESD at higher levels of care and lend support to having specialty treatment programs for patients with BESD. International Registered Report Identifier (IRRID) DERR1-10.2196/32270