This second phase marked the definitive integration of the CEHE into the academic sphere, achieved through its incorporation—while retaining some autonomy—into the Faculty of Theology of the Portuguese Catholic University in 1984. Earlier plans in the previous decade to make LS an official publication of the Faculty had not come to fruition. Later, in 1989, the CEHE was transformed into the CEHR following the election of its first board of directors in 1988. This institutional restructuring contributed to both the expansion and consolidation of a network of researchers focused on religious studies, encompassing the full diachronic scope of classical historiographical periodisation.

LS continued to be published in Lisbon and reflected, in its leadership and editorial committees, the composition of the CEHR’s governing body. Successive directors included António Montes Moreira, Carlos Moreira Azevedo, Manuel Clemente—each a Catholic prelate—followed by Ana Maria Jorge, António Matos Ferreira, and Paulo Oliveira Fontes. As in its earlier phase, the magazine was intended to be published annually. This goal was largely met, with exceptions for biennial volumes in 1996–1997 (VIII–IX), 2001–2002 (XIII–XIV), and 2007–2008 (XIX–XX). In 2011 (XXIII), LS transitioned to a biannual publication.

Unlike the 1st Series, which primarily addressed individual articles without a unifying structure, the 2nd Series aimed to unify its volumes thematically or chronologically. Chronological themes were particularly common until the 20th volume, covering the mediaeval, modern, and contemporary periods in sequence.

Each volume included articles along with supplementary sections: Crónica Universitária [University Chronicle], a section for book reviews, and, starting with volumes VIII–IX (except for volume XXI, dedicated to the magazine’s 50th anniversary), a section entitled Notas de Investigação [Research Notes].

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