Anxiety and depression in youth are highly prevalent and often comorbid. Transdiagnostic interventions have been developed to treat anxiety and depression simultaneously, but questions remain as to what extent these interventions are equally effective across different patterns of anxious-depressed comorbidity. The current study re-analyzed data from a transdiagnostic randomized controlled trial (RCT) to better understand the characteristics and trajectories of comorbid anxious-depressed versus anxious-only youth. Archival data was used from an RCT that examined the effects of a brief behavioral transdiagnostic intervention (BBT) for anxiety and depression based in pediatric primary care compared to referral to outpatient care (ARC). The current study analyzed a subsample 175 youth (ages 7-16 years, M = 11.1, SD = 2.5; 57.7% Female; 68.6% Caucasian). Clinical outcomes (i.e., anxiety, depression, functioning) were assessed at baseline, post-treatment, and at follow-up. Baseline differences by depression status (anxious-depressed vs. anxious-only) were examined using t-tests and chi-squared tests. Multiple linear regression was used to examine moderation by depression status at specific timepoints. Follow-up analyses included baseline covariates that differed by depression status and tested higher-levels interactions with these variables. At baseline, anxious-depressed youth were significantly more likely to be older, female, have higher clinical severity, and greater psychosocial disadvantage. Depression status did moderate effects on anxiety at follow-up (p = .015). BBT was significantly superior to ARC in reducing anxiety among anxious-only youth (p < .001) but not among anxious-depressed youth (p = .99). Follow-up analyses added covariates and uncovered a significant three-way interaction with treatment, depression status, and trauma (p = .028). BBT was significantly superior to ARC in reducing anxiety in all subgroups except for anxious-depressed youth with a history of trauma. The results illustrate the overall superiority of the BBT intervention across clinical domains and across a wide variety of participant characteristics. As hypothesized, comorbid depression did moderate treatment effects but only on anxiety at the follow-up assessment, and only for youth with both comorbid depression and a history of trauma. Future work should investigate whether modifications to the content of transdiagnostic interventions are merited in order to address the poorer outcomes for this group.