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Background: Posttraumatic stress disorder (PTSD) and substance use disorders (SUD) commonly co-occur. Several treatments for co-occurring PTSD and SUD (PTSD + SUD) exist, yet evidence for comparative treatment effectiveness is restricted by a historical emphasis on symptom severity and substance consumption endpoints instead of recovery-oriented outcomes. Moreover, extant syntheses relied on conventional analytic approaches prioritizing standardized mean group differences, instead of clinically significant change (CSC), and included few pharmacological randomized clinical trials (RCTs).Objective: In an extension of Project Harmony (R01AA025853), this study (R01DA061338) will apply novel quantitative approaches addressing limitations of prior work to elucidate which PTSD + SUD treatments work best overall and at the individual level.Method: This study will harmonize data from over 60 RCTs (N > 8,000) and use meta-analysis of individual patient data, integrative data analysis, and propensity score weighting to assess the comparative effectiveness of pharmacological, behavioral, and combination treatments for PTSD + SUD. Clinical severity outcomes will be measured as latent PTSD symptom severity, alcohol consumption, and other drug consumption. Recovery outcomes will be estimated from indicators of psychosocial functioning and substance use consequences. State-of-the-art CSC methodologies will be used in analyses of the original Project Harmony dataset (36 RCTs; N = 4,046), which will evaluate the proportion of patients in each treatment class that showed (non)significant improvement or worsening along clinical and recovery outcomes. Analyses of the expanded Project Harmony dataset will assess comparative effectiveness of active PTSD + SUD treatment classes, compared to treatment as usual, on clinical severity and recovery outcomes.Conclusions: By applying modernized quantitative methodologies to patient-level data from at least 60 RCTs, this study will advance the field's understanding of which PTSD + SUD treatment approaches are most effective across multiple indicators (i.e. clinical severity and recovery outcomes). This study is registered in the International Prospective Register of Systematic Reviews (PROSPERO identifier CRD420251250349).