Although prevalence of developmental dyscalculia is estimated between 5% and 7%, it did not receive a great deal of public recognition as in the case of dyslexia. This factor, added to the lower availability of studies regarding this specific learning disorder, increases difficulties in inclusive classrooms, where teachers are required to meet heterogeneous educational needs. At present, educational interventions for dyscalculia are demanded to practitioners outside schools, due to a lack of didactical instruments that can help teachers in their daily work, especially during primary school years, when diagnosis of dyscalculia is made. This article presents a case study involving two primary school students, attending an Italian public school, one with dyscalculia and one with difficulties in mathematics. Based on recent studies of cognitive and developmental neuroscience, an educational intervention has been proposed to support and reinforce the understanding numerosities, as an essential skill to build further mathematical knowledge. According to the learning by doing approach, several activities with manipulatives specifically designed for mathematical learning (ArtecBlocks, interlocking cubes) were proposed to the students, in order to combine gamified manual activity with the opportunity of learning by doing, supporting intrinsic motivation while decreasing math anxiety. Following a one-month training, the student with difficulties in mathematics showed limited improvements, probably due to an increase in her confidence, while the student with dyscalculia showed significant improvements not only in counting, but also in calculation procedures and recall of arithmetic facts, with an increase in accuracy and control over the result and a reduction in response times. Findings suggest the feasibility of the learning by doing approach with the use of manipulatives, which enhances inclusion and learning personalization, but also confidence towards mathematics.