Enhancing the effectiveness and efficiency of national research systems is a top priority on the policy agendas of many countries. This study focuses on one aspect of the macroeconomic efficiency of research systems: whether research institutions specialize in scientific domains where they have a competitive advantage. To evaluate this, we developed a novel methodology. This methodology measures the scientific specialization indices of each organization in various research fields and assesses their relative research productivity. It then examines the correlation between these scores and between the resulting rankings. We applied this methodology to Italian universities. We found that a significant rank correlation between universities’ field specialization and their performance appears only in a few areas, and overall, the rankings are completely unrelated. Providing such data to research managers and policymakers can help inform strategies to enhance both micro- and macro-level efficiency.