Even in primary school, mathematics achievement depends upon the efficiency of cognitive, metacognitive and self-regulatory processes. Thus, for pupils to carry out a computation, such as a written calculation, metacognitive mechanisms play a crucial role, since children must employ self-regulation to assess the precision of their own thinking and performance. This assessment, in turn, can be helpful in the regulation of their own learning. In this regard, a body of literature suggests that the application of psychoeducational interventions that promote the development of mathematics-related metacognitive (e.g., control) processes, based on the analysis of the students' errors, can successfully influence mathematics performance. The main objective of the current study was to investigate the impact of a metacognitive and cognitive training program developed to enhance various arithmetic skills (e.g., syntax, mental and written calculation), self-regulatory and control functions in primary and secondary school students exhibiting atypical mathematical development. Sixty-eight Italian children, 36 male and 32 female (mean age at pretest = 9.3 years, SD = 1.02 years), meeting the criteria for the diagnosis of dyscalculia or specific difficulties in mathematics, took part in the study. Of these, 34 children (i.e., experimental group) underwent the cognitive and self-regulatory intervention enhancing mathematics skills training for 16 weekly sessions. The remaining students were assigned to the control group. For a pre-test and post-test, a battery of standardized mathematical tests assessing different mathematics skills, such as written and mental operations, digit transcription and number ordering skills, was administered and provided a series of measures of calculation time and accuracy (i.e., number of errors). In the post-test, the experimental group exhibited better accuracy in written calculation and in digit transcription. Overall, the current outcomes demonstrate that psychoeducational interventions enriching metacognitive and mathematical achievements through error analysis may be an effective way to promote both the development of self-regulatory and control skills and mathematical achievement in children with atypical mathematical development.