Current neural models of autism spectrum disorder (ASD) and anxiety disorders suggest hyperactivation of amygdala in anxiety, but hypoactivation of amygdala in ASD. The objectives of this study were to (i) test the hypothesis that amygdala activity measured by functional magnetic resonance imaging (fMRI) represents a hybrid signal of opposing social functions and anxiety symptoms, and (ii) determine whether longstanding findings of decreased amygdala activation in ASD apply only to those individuals with ASD and low levels of anxiety. During fMRI scanning, 81 youth with ASD and 67 non-ASD control participants completed a face recognition paradigm that elicits robust amygdala activation. Only individuals with ASD and low anxiety levels (a subsample of 28 participants) showed decreased amygdala activation relative to controls. In the ASD group, anxiety symptoms were positively correlated with amygdala activity across the full ASD group, whereas core ASD symptoms (including social deficits) were negatively correlated. Results indicate that hypoactivation of amygdala in ASD, a suggestive finding first reported nearly 20 years ago, can be masked by comorbid anxiety—thus bringing enhanced clarity to this line of work. Amygdala activity represents a hybrid signal of emotion and social processes that cannot be reduced to either alone.