Objective: Naturalistic and neurophysiological assessments are relevant as outcome measures in autism intervention trials because they provide, respectively, ecologically valid information about functioning and underlying neurocognitive mechanisms. We conducted a systematic review to highlight which specific neurophysiological techniques, experimental tasks, and naturalistic protocols have been used to assess neural and behavioral functioning in autism intervention studies. Methods: Studies were collected from four electronic databases between October 2019 and February 2020: MEDLINE (via PubMed), PsycINFO, LILACS, and Web of Science, and were included if they used structured observational, naturalistic, or neurophysiological measures to assess the efficacy of a nonpharmacological intervention for ASD. Results: Fourteen different measures were used by 64 studies, with the Autism Diagnostic Observation Schedule the most frequently used instrument. Thirty-seven different coding systems of naturalistic measures were used across 51 studies, most of which used different protocols. Twenty-four neurophysiological measures were used in 16 studies, with different experimental paradigms and neurophysiological components used across studies. Conclusions: Cross-study variability in assessing the outcomes of autism interventions may obscure comparisons and conclusions about how different behavioral interventions affect autistic social communication and underlying neurophysiological mechanisms.