The first diocesan temple in Pamplona saw its furnishings strongly reformed since the beginning of the 19th century, following the recommendations of the men of academicism, in order to replace the baroque altarpieces with others of classical style. The post-war intervention was another important moment in the removal of altarpieces from its interior. 

The main altarpiece, late Gothic, was sold when Bishop Zapata undertook the construction of a new one in the style of the Escorial aesthetics, in 1596. The old one, with seven painted panels, had been paid for at the beginning of the 16th century by Queen Catalina, and was moved to the parish of Echalar in 1599. The painter Miguel de Salazar was in charge of the conduction and assembly work, for which he was to be paid the important sum of 200 ducats. The non-fulfillment of the payments motivated a lawsuit with the steward of the first prize of that locality of the Valley of Larráun. The cost of the transfer was estimated at 22 ducats, so we suspect that the painter would add some panels, or else the adaptation would require a great deal of work. To enlarge the dimensions of the altarpiece, a body was added by Juan de Angulo. The piece was definitively lost track of when the main altarpiece of academic style was made (1785-1787).

Another altarpiece was sent to Muguiro from the cathedral, specifically the one dedicated to Saint Blaise, in 1848. The new altarpiece of the saint in Pamplona, designed in Madrid, housed a canvas by Buenaventura Salesa, which is preserved in the cathedral, although the altarpiece was moved to the parish of San Juan Bautista de Burlada in the mid-twentieth century. 

The Renaissance altarpiece is conserved in Muguiro. It is a A piece of Aragonese resonances and exquisite and very fine carving of grotesques and laurels, with a design in which oculi are superimposed on the niches of clear Florentine inspiration. Its chronology should be placed around 1530, in parallel to the execution of the choir stalls, although its quality is considerably superior. The board of trustees of the chapel of San Blas in the cathedral belonged to the Caparroso family and, later, to the Counts of La Rosa.

The third altarpiece that left the cathedral walls was the largest, as a consequence of the post-war intervention (1940-1946) and against the criterion of the technicians. After being dismantled for some years and its sale for the cathedral of Calahorra or the parish of the Assumption of Cascante was discarded, it was acquired by the Diputación Foral and was destined to the parish of San Miguel de Pamplona where it was mounted, without the jasper base that contained a very interesting registration in which the munificence of the bishop Antonio Zapata, not only as patron of the work, but also as mentor of all its iconographic program, was given account of.

Two other altarpieces, in this case, baroque altarpieces from two cathedral chapels, were also moved to different places. The guidelines proposed to the chapter by Santos Ángel de Ochandátegui, at the end of the works on the façade, to beautify the temple, in 1800, with a clearly Jansenist inspiration, contemplated the elimination of the altarpieces, with these words: "It is assumed that the altarpieces of very coarse carving that the chapels have must necessarily be removed and that others of noble and simple architecture must be executed, composed of two columns and a proportionate finial, with framework for a painting or a niche for a statue, or alternating one and the other, imitating the work of marbles and bronzes, when it cannot be built of these materials."

The altarpiece of San Martín, the work of José de San Juan y Martín (1699-1700) from Tudela, has been in the parish of Yaben since 1805, presiding over the main chapel.

The one that presided over the chapel of the Holy Trinity, board of trustees of the Constables of Navarre and work of Pedro Soravilla (1713), presides since 1805 the parish of Errazquin, where it was moved by the initiative of its abbot, Don Juan Bautista Artola.

With the passage of time, the altarpieces of classical style, made at the beginning of the 19th century to replace the baroque ones, did not have a better fate. In the summer of 1804, Canon Joaquín María Pitillas was delegated to choose the sculptor who would make them. The favorite painter in those years, Buenaventura Salesa, made the canvases of the altarpieces of St. Blas, St. Vincent and St. Christina, which have survived in part, as well as some of the sculptures. The altarpieces suffered a worse fate, except for that of St. Blaise, which, as we have noted, was moved to Burlada. Of those of St. John the Evangelist and St. Martin, only photographs are preserved.