Research fronts (RFs) represent the most dynamic areas of science and technology and the topics that receive higher attention in a specific field. Their identification has become the focus of global scientific and technological competition. In this study, we performed an analysis of the In-Cites RFs from Web of Science (WoS) in seven Spanish universities as a case study in the period 2015–2019. Our purpose is threefold: (1) to develop a methodology for approximating the ‘alignment’ of scientific articles with the RFs, (2) to test if Highly Cited Papers (HCP) from these universities are more aligned with RFs than the rest of the output, and (3) to test if papers aligned with RFs receive more citations per document than those not aligned. The study uses a novel retrieval method, and the analysis is conducted using a coincidence method (comparison with a standard), in which Mann–Kendall’s test and Pearson’s correlation are used. The results show that there is alignment between output and the HCP and those better aligned, present greater mean ranks of citations per article. This study shows the usefulness of RFs for orienting the research priorities at the institutional level for the university.