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Laguérie was ordained a priest on 29 June 1979 by Marcel Lefebvre, founder of the Society of St. Pius X. In 1984 he succeeded François Ducaud-Bourget as priest in charge of the Saint-Nicolas-du-Chardonnet in Paris, and remained there until 1997. In 2002, he moved to Bordeaux where he illegally squatted the Saint-Eloi Church, before he re-examined his situation due to the creation of the Pontifical Commission Ecclesia Dei which had been established in 1988 by Pope John Paul II to re-establish contacts with the Society of Saint Pius X.
On 16 September 2004, Laguérie was dismissed from the Society by his superior bishop Bernard Fellay. Some 2 years later, on 8 September 2006, he was chosen as leader of the newly founded Institut du Bon Pasteur, which received Pope Benedict XVI's approval, thus regularizing the situation of the Saint-Eloi Church following a signed convention with the archbishop of Bordeaux, Jean-Pierre Ricard.