BACKGROUND: Patients with chronic disease represent an at-risk group in the face of the COVID-19 crisis as they need to regularly monitor their lifestyle and emotional management. Coping with the illness becomes a challenge due to supply problems and lack of access to health care facilities. It is expected these limitations, along with lockdown and social distancing measures, have affected the routine disease management of these patients, being more pronounced in low- and middle-income countries with a flawed health care system. OBJECTIVES: The purpose of this study is to describe a protocol for a randomized controlled trial to test the efficacy of the Adhera® MejoraCare Digital Program, an mHealth intervention aimed at improving the quality of life of patients with chronic diseases during the COVID-19 outbreak in Paraguay. METHOD: A two-arm randomized controlled trial will be carried out, with repeated measures (baseline, 1-month, 3-month, 6-month, and 12-month) under two conditions: Adhera® MejoraCare Digital Program or waiting list. The primary outcome is a change in the quality of life on the EuroQol 5-Dimensions 3-Levels Questionnaire (EQ-5D-3L). Other secondary outcomes, as the effect on anxiety and health empowerment, will be considered. All participants must be 18 years of age or older and meet the criteria for chronic disease. A total of 96 participants will be recruited (48 per arm). CONCLUSIONS: It is expected that the Adhera® MejoraCare Digital Program will show significant improvements in quality of life and emotional distress compared to the waiting list condition. Additionally, it is hypothesized that this intervention will be positively evaluated by the participants in terms of usability and satisfaction. The findings will provide new insights into the viability and efficacy of mHealth solutions for chronic disease management in developing countries and in times of pandemic. TRIAL REGISTRATION: ClinicalTrials.gov NCT04659746.