It is acknowledged the need for interventions to improve reading comprehension and its cognitive underpinnings, such as executive functions. The present study implemented a computerized cognitive training for enhancing reading comprehension in primary school children through EF activities embedded in text comprehension exercises. 263 third and fourth graders were involved in this study and randomly divided into experimental (n = 156, M[subscript age] = 9.06, SD = 0.62) and control (n = 107, M[subscript age] = 9.21, SD = 0.63) groups. All the children of the experimental group attended 9 training sessions, twice a week, for approximately 1 h and 30 min each within the school context during teaching hours. The intervention proposed several exercises requiring EF processes implicated in text comprehension (e.g., identifying incongruences in the text, ordering events) through a metacognitive approach. The intervention was as standardized as possible through digitalization of the activities and videotaped explanations and demonstrations. The intervention proved to be feasible and effective in enhancing processes relevant for reading comprehension, verbal updating working memory, and nonverbal reasoning, and individual differences in pre-test performances and EF predicted the gains obtained by the training. The study provides a good model of intervention on the cognitive control processes underpinning text comprehension in primary graders.