Purpose: This study provides a new look at the late 19th-century university issue in Spain. Loss of self-government among universities and the state's centralization brought a conflict between science and religion to the fore in the process of the secularization of knowledge. Design/methodology/approach: We first delve into the anti-Darwinian framework associated with the scientific professionalization process, focusing on the case of the jurist Antonio Hernández Fajarnés (1851-1909). Secondly, we study the idea of the university that emerged from the "Ateneo de Madrid," analyzing key speeches from the jurist Francisco Fernández de Henestrosa (1855-s.d.) given in 1887/88 and from the pharmacist José Rodríguez Carracido (1856-1928). Findings: The study concludes that the Restoration Era in Spain was characterized by a generalized desire -- shared by neo-Scholastics, conservatives and liberal rationalists -- to improve the public university system. In this context, French influence was no doubt decisive; however, the Humboldtian university idea had already begun to have notable influence. Originality/value: This article analyzes sources yet unknown to international research, such as the "Ateneo de Madrid" debates and Spanish university rectors' inaugural speeches. It opens up a critical examination of the so-called displacement of educational principles in Spain toward a state-centered system of doctrinal "moderantismo" as opposed to the nation-centered system of the Cádiz liberalism. At the same time, it identifies key pockets of resistance relative to Spanish university transformation toward increased methodological secularization.