Although deficits in emotion regulation have been implicated in the maintenance of binge eating, few prospective studies have examined longitudinal associations between emotion regulation and eating disorder symptoms, which are needed to test these theoretical models. Using a naturalistic design, the current study utilized longitudinal multilevel analyses to examine whether improvements in emotion regulation during treatment are associated with decreased binge eating frequency and eating disorder cognitions in a heterogeneous sample of adults with binge eating (N = 97). Analyses also accounted for between- and within-person differences in negative affect to inform specific targets for intervention. Significant within-person associations between emotion regulation, negative affect, and eating disorder severity support hypotheses that emotion dysregulation and negative affect co-occur with eating disorder psychopathology. Only between-person differences in negative affect demonstrated associations with binge eating frequency over time. Data suggest that momentary interventions targeting negative affect and emotion regulation skills may decrease eating disorder cognitions, but not binge eating frequency, among adults with binge eating.