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<b>Background</b>: The BEST study investigated the effectiveness of a 12-week digital treatment program for male LUTS. Here, we report on the long-term outcomes of the patients involved in this trial. <b>Methods</b>: The randomized controlled BEST trial enrolled 237 patients (intervention group, IG: n = 112, hereafter referred to as the direct intervention group [DIG]; control group, CG: n = 125, hereafter referred to as the postponed intervention group [PIG]). The intervention consisted of pelvic floor muscle training, behavioral training, completion of a micturition diary, bladder training, urge suppression techniques, fluid and dietary management, and structured educational content. Patients in the DIG received the intervention immediately, Patients in the PIG after a 12-week waiting period. Patients in both groups were offered the option to complete additional treatment cycles at their discretion. The primary endpoint was change from baseline in the International Prostate Symptom Score (IPSS). Secondary endpoints included the symptom severity (OAB-q SF1) and quality-of-life (OAB-q SF2) subscales of the Overactive Bladder Questionnaire, among others. Long-term follow-up assessments at 24, 36, and 48 weeks for participants in both study arms were prospectively specified in the study protocol. <b>Results</b>: Baseline data from 236 patients were available for the follow-up analyses. In a linear mixed-effects model, the fixed effect of time on IPSS was found to be statistically significant (F(4, 515.245) = 89.77, <i>p</i> < 0.001), indicating differences across measurement time points. Compared with the baseline, IPSS scores were lower at all subsequent follow-up assessments. The mean difference between the baseline and 12 weeks after was -6.32 points (95% CI: -7.60 to -5.04; <i>p</i> < 0.001). Differences between the baseline and 24 weeks (-7.81 points; 95% CI: -9.37 to -6.25; <i>p</i> < 0.001), baseline and 36 weeks (-8.62 points; 95% CI: -10.46 to -6.79; <i>p</i> < 0.001), and baseline and 48 weeks (-9.56 points; 95% CI: -12.66 to -6.46; <i>p</i> < 0.001) were also statistically significant. Comparable patterns of improvement were observed for both subscales of the OAB-q Short Form questionnaire. In a separate linear mixed-effects model, the fixed effect of time on IPSS after the discontinuation of app usage was not statistically significant (F(2, 19.750) = 0.01, <i>p</i> = 0.992), suggesting stable effects after discontinuation. <b>Conclusions</b>: Long-term outcomes of the structured app-based therapeutic program demonstrated that a multimodal digital intervention for male LUTS induces a rapid and clinically meaningful symptom reduction within the first 12 weeks, with consolidating and sustaining benefits over up to 48 weeks.