This pilot study evaluated the use of smartphone ecological momentary assessments (EMA) for self-monitoring to optimize treatment outcomes among gay and bisexual men enrolled in an outpatient methamphetamine abuse treatment service program. Participants (N = 34) received EMA prompts five times daily to self-monitor their methamphetamine use, cravings, sexual risk behaviors, and associated triggers and affect throughout the 8-week treatment program. Participants were randomized into either a self-directed condition with access to a web-based EMA response visualization dashboard ("EMA + Dashboard"; n = 16); or, a counselor-supported condition incorporating weekly, 30-min, one-on-one counseling sessions to review and discuss the participant's self-monitoring data on the dashboard ("EMA + Dashboard + Counselor"; n = 18). Pilot participants were compared with historical controls (n = 102) as the reference group in multiple regression analyses to assess the impact of the two study conditions on the treatment service program outcomes. Study participants with weekly counseling (EMA + Dashboard + Counselor) exhibited significantly greater reductions in the number of condomless anal intercourse episodes than historical controls (IRR = 0.02, 95% CI [0.00, 0.30]), whereas the reduction was of similar magnitude as controls in the EMA + Dashboard self-directed condition (IRR = 0.23, 95% CI [0.02, 3.56]). Treatment effects were not significant for comparisons between the two study conditions and historical controls for self-reported methamphetamine use (EMA + Dashboard: IRR = 1.06, 95% CI [0.32, 3.49]; EMA + Dashboard+Counselor: IRR = 0.46, 95% CI [0.14, 1.49]), number of male partners (EMA + Dashboard: IRR = 1.02, 95% CI [0.39, 2.61]; EMA + Dashboard+Counselor: IRR = 0.54, 95% CI [0.20, 1.45]), and the likelihood of providing a urine sample that tested positive for methamphetamine metabolites (EMA + Dashboard: OR = 1.00, 95% CI [0.79, 1.25]; EMA + Dashboard + Counselor: OR = 0.93, 95% CI [0.74, 1.16]). The pilot study provides preliminary evidence that the treatment outcome for condomless anal intercourse can be improved through a combination of smartphone- and counselor-assisted self-monitoring.