This manuscript deals with how cooperative learning in pre-school and primary education can be dimensionalized in terms of reducing gender differences and inequalities. In this study, formulated through instructional approaches delivered in four medium- to very high-complexity schools (the number of students with an immigrant background ranging from 30% to 100%), 376 pre-service teachers and 43 qualified teachers were asked to analyze the instruction that they gave to 1658 pre-school and primary students over two consecutive years. Instruction was defined in terms of contextualized physical education challenges that included cooperative psychomotor physical challenges, guided discovery activities and psychomotor problem-solving. The analysis was based on reflective narratives on both gender differences and inequalities, which evinced 792 comments regarding gender (618 by the pre-service teachers and 174 by the schoolteachers) and 627 comments for inequalities (363 by the pre-service teachers and 264 by the schoolteachers). The analysis produced categories based on critical reflection—on both individual and classroom scales—from the pre-service teachers and the schoolteachers. Each of the cooperative learning dimensions, i.e., positive interdependence, individual accountability, promotive interaction, social skills, and group processing, were investigated to produce a set of principles and competencies that best promoted education for sustainable development. The research produced 42 principles that operated under the tenet of leave-no-one-behind, with positive interdependence and promotive interaction providing the higher number of principles that are best suited to tackle, through cooperation processes, equity and inclusivity issues in pre-school and primary education classrooms.