When his father was killed in the disastrous Expedition of Mostaganem (1558), Alfonso became the new governor and captain general of Oran and Mazalquivir.
In 1561, Alfonso was able to finally free his younger brother Martin who had been taken prisoner by the Algerians at Mostaganem, after paying a ransom of 23,000 escudos.
He reinforced the fortification and defense of the cities of Oran and Mazalquivir, which were attacked and besieged by a huge Algerian army in April 1563.
After this successful battle, Alfonso was appointed Viceroy of Navarre by King Philip II on 5 September 1564.
At the end of November, Alcaudete arrived in Navarra, but died of tuberculosis a little later, without even having reached his court at Pamplona.