On Christmas 1493, the count blocked the access of the king and queen to the capital city, but after a fleeting peace agreement was reached, the ceremony was held.

In 1512, Navarre was invaded by a combined Castilian-Aragonese army sent by Ferdinand II of Aragon, whose second wife was Germaine de Foix (1490–1538), a cousin of Queen Catherine.

The Castilian troops commanded by the duke of Alba crossed the Pyrénées onto Lower Navarre capturing St-Jean-Pied-de-Port on 10 September 1512 and wreaking havoc across much of the merindad.

Following the invasion, Navarre south of the Pyrenees was annexed to Castile nominally as an autonomous kingdom (aeque principalis) by the victorious Ferdinand after taking an oath to respect the Navarrese laws and institutions (1515).

Depressed by the defeats and adverse diplomatic results, John III died at the castle of Esgouarrabaque in Monein, Béarn, on 14 June 1516 after lying gripped by fatal fevers.