Sebastiaõ's mother remarried two decades later, in 1838, her uncle, Don Carlos María Isidro, the first Carlist pretender to the throne of Spain.

On January 15, 1837, during the First Carlist War, the then 23-year-old Sebastian was excluded, by law of the Cortes, ratified by royal decree of Queen Regent Maria Christina, from the Spanish succession, on the grounds that he had joined Don Carlos' rebellion against Isabella II of Spain.

Following his mothers marriage to Don Carlos in 1838, he became heir presumptive to the Portuguese throne per Miguelist reckoning, and would remain so until the birth of his cousin Infanta Maria das Neves in 1852.

When widowed at the age of 50 he remarried, on 19 November 1860, his cousin Infanta María Cristina of Spain, the niece of his first wife, and two decades his junior.

After the overthrow of Isabella II of Spain in 1868 Sebastian moved to Pau, where he tried to reconcile with the Carlist branch of the House of Bourbon, without success.