Joan I's marriage to the future Philip IV in 1284 joined her inherited rule of Navarre and Champagne to the French royal dynasty. She became queen consort of France when Philip succeeded in 1285, while remaining queen of Navarre and countess of Champagne in her own right. Navarre was governed in her name by French administrators. Their authority and her continuing absence aroused local resentment, although Navarrese allegiance to Joan as sovereign endured.

Her involvement was more direct in Champagne, which she visited and whose revenues and administration she defended. In 1297, accounts credit her with raising forces against Henry III, Count of Bar, after his invasion of the county, and with having him imprisoned. She also pursued accusations of financial wrongdoing against Guichard, bishop of Troyes. Her authority in her own lands coexisted with Philip's growing intervention, and her attempts to influence his wider policies were limited.

Joan used patronage to support religious communities, learning, and charitable provision. She provided for the foundation of the Collège de Navarre in Paris in 1305, with support for students in grammar, arts, and theology. Her confessor Durand of Champagne wrote the Speculum Dominarum for her, and she encouraged Jean de Joinville to compose his account of Louis IX, completed after her death. Her final will also made provision for a hospital at Château-Thierry. She died in 1305, leaving her son Louis to inherit Navarre and Champagne.