Introduction: Motor competence is a fundamental component of children’s physical development, influencing lifelong physical activity and overall health. Schools play a key role in fostering motor competence through physical education; however, evidence on effective instructional models remains scarce, particularly at the primary school level in Portugal. Objective: This study evaluated the impact of a professional development program for generalist primary school teachers, with and without co-teaching involving specialist physical education teachers, on students’ basic motor competencies. Methodology: This quasi-experimental study included 26 teachers and 220 students, assigned to three groups: professional development plus co-teaching, professional development only, and a control group. The intervention included a 25-hour accredited program and eight weeks of physical education co-teaching. Students’ motor competence was assessed pre- and post-intervention using the MOBAK test battery. Results were analyzed using repeated measures ANOVA. Propensity score matching was applied to improve group comparability. Results: All groups demonstrated significant improvements in motor competence. No additional benefits were observed for the intervention groups compared to the control. Discussion: The COVID-19 pandemic disrupted the study timeline, delaying the start and shortening the intervention period, which may have influenced its impact. While professional development and co-teaching remain promising strategies, the non-randomized design and variability in implementation may have influenced the outcomes. Conclusions: This study provides early evidence on the implementation of co-teaching in primary physical education settings in Portugal. Future research should systematically compare co-teaching with other instructional models, incorporate process control, and include follow-up assessments to determine effective, sustainable approaches for improving motor competence and informing educational policy and practice.