Background Lack of physical activity (PA) and sedentary behaviors are leading risk factors for noncommunicable diseases (NCDs). Web- and smartphone-based interventions are effective in increasing PA in older adults and in patients with NCD. In many countries, spa therapy, commonly prescribed to patients with NCD, represents an ideal context to initiating lifestyle changes. Objective This study aimed to evaluate, in patients attending spa therapy, the effectiveness of an intervention combining a face-to-face coaching and, when returning home, a web- and smartphone-based PA program on the achievement of PA guidelines (PAG) 12 months after the end of spa therapy. Methods This was a 12-month, prospective, parallel-group randomized controlled trial. Patients were enrolled during spa therapy and randomized 1:1 to intervention or control group who received PA usual advice. From the end of spa therapy, PA, weight, waist circumference, and quality of life of the participants were assessed by phone every 2 months. Primary outcome was meeting PAG (PA ≥600 metabolic equivalent of task) at 12 months. Secondary outcomes were meeting current PAG at 6 months; sedentary time, weight, waist circumference, PA, and quality of life at 6 and 12 months. Objective use data of the web- and smartphone-based PA program were collected. Analytic methods included intention to treat and constrained longitudinal data analyses. Results The study sample included 228 participants (n=176, 77.2% females) with a mean age of 62.4 (SD 6.7) years and a mean BMI of 28.2 (SD 4.2) kg/m2. Approximately 53.9% (123/228) of the participants were retired. No group differences were found for any baseline variable. At 12 months, the proportion of patients achieving PAG was significantly higher in intervention group than in the control group (81% vs 67% respectively, odds ratio 2.34, 95% CI 1.02-5.38; P=.045). No difference between intervention and control group was found neither in achieving PAG at 6 months nor for sedentary time, weight, and waist circumference at 6 and 12 months. Regarding quality of life, the physical component subscale score was significantly higher at 12 months in the intervention group than in the control group (mean difference: 4.1, 95% CI 1.9-6.3; P<.001). The mean duration use of the program was 7.1 (SD 4.5) months. Attrition rate during the first 2 months was 20.4% (23/113) whereas 39.8% (45/113) of the participants used the program for at least 10 months. Conclusions PA increased in both the intervention group and the control group. However, at 12 months, more participants met PAG in the intervention group compared with the controls. This indicates that the web- and smartphone-based program could have maintained PA in the intervention group. In addition, a spa therapy seems to be an ideal time and framework to implement PA education. Trial Registration ClinicalTrials.gov NCT02694796; https://clinicaltrials.gov/ct2/show/NCT02694796