Abstract Background Alcohol abuse, other substance use disorders, and risk behaviors associated with the human immunodeficiency virus (HIV) represent three of the top 10 modifiable causes of mortality in the US. Despite evidence that continuing care is effective in sustaining recovery from substance use disorders and associated behaviors, patients rarely receive it. Smartphone applications (apps) have been effective in delivering continuing care to patients almost anywhere and anytime. This study tests the effectiveness of two components of such apps: ongoing self-monitoring through Ecological Momentary Assessments (EMAs) and immediate recovery support through Ecological Momentary Interventions (EMIs). Methods/design The target population, adults enrolled in substance use disorder treatment (n = 400), are being recruited from treatment centers in Chicago and randomly assigned to one of four conditions upon discharge in a 2 × 2 factorial design. Participants receive (1) EMAs only, (2) EMIs only, (3) combined EMAs + EMIs, or (4) a control condition without EMA or EMI for 6 months. People in the experimental conditions receive smartphones with the apps (EMA and/or EMI) specific to their condition. Phones alert participants in the EMA and EMA + EMI conditions at five random times per day and present participants with questions about people, places, activities, and feelings that they experienced in the past 30 min and whether these factors make them want to use substances, support their recovery, or have no impact. Those in the EMI and EMA + EMI conditions have continual access to a suite of support services. In the EMA + EMI condition, participants are prompted to use the EMI(s) when responses to the EMA(s) indicate risk. All groups have access to recovery support as usual. The primary outcome is days of abstinence from alcohol and other drugs. Secondary outcomes are number of HIV risk behaviors and whether abstinence mediates the effects of EMA, EMI, or EMA + EMI on HIV risk behaviors. Discussion This project will enable the field to learn more about the effects of EMAs and EMIs on substance use disorders and HIV risk behaviors, an understanding that could potentially make treatment and recovery more effective and more widely accessible. Trial registration ClinicalTrials.gov, ID: NCT02132481 . Registered on 5 May 2014.