Background CUIDA-TE is an APP that offers transdiagnostic cognitive behavioral therapy focused on enhancing emotion regulation. As a novelty, it incorporates ecological momentary interventions (EMI), which can provide psychological support in real time, when suffering arises. The main goal of the study is to evaluate the efficacy of CUIDA-TE to improve emotion regulation in healthcare workers, a population that has been particularly emotionally impacted by the COVID-19 pandemic. Methods In this three-arm, randomized controlled trial (RCT) the study sample will be composed of a minimum of 174 healthcare workers. They will be randomly assigned to a 2-month EMI group (CUIDA-TE APP, n ≥ 58), a 2-month ecological momentary assessment (EMA) only group (MONITOR EMOCIONAL APP, n ≥ 58), or a wait-list control group (no daily monitoring nor intervention, n ≥ 58). CUIDA-TE will provide EMI if EMA reveals emotional problems, poor sleep quality/quantity, burnout, stress, or low perceived self-efficacy when regulating emotions. Depression will be the primary outcome. Secondary outcomes will include emotion regulation, quality of life, and resilience. Treatment acceptance and usability will also be measured. Primary and secondary outcomes will be obtained at pre- and post-intervention measurements, and at the 3-month follow-up for all groups. Discussion To our knowledge, this is the first RCT that evaluates the efficacy of an APP-based EMI to improve emotion regulation skills in healthcare workers. This type of intervention might ultimately help disseminate treatments and reach a larger number of individuals than traditional face-to-face individual therapies. Trial registration ClinicalTrial.gov: NCT04958941 Registered 7 Jun 2021.