In 1560, he joined the army of Philip II and for more than 15 years fought in the Low Countries under the command of Fernando Álvarez de Toledo, Duke of Alba.
As the effective agent of Philip's interventionist foreign policy, Mendoza acted in concert with the Catholic League for which he acted as paymaster by funnelling Habsburg funds to the Guise faction; he encouraged it to try, by popular riots, assassinations, and military campaigns, to undercut any moderate Catholic party that offered a policy of rapprochement with the Huguenots.
[1] His role in backing the extremist Catholic House of Guise became so public that King Henry III demanded his recall.
Many of his dispatches to Madrid were first deciphered only in the Simancas archives by De Lamar Jensen;[3] they revealed, for the first time, Mendoza's role in organising and co-ordinating the Paris riots led by the Duke of Guise, known as the Day of the Barricades (12 May 1588), which had been presented as a spontaneous rising of the people and timed to coincide with the sailing of the Spanish Armada.
Bernardino also published a book on the art of warfare, under the title Theórica y práctica de la guerra and a Spanish translation of the Politicorum sive civilis doctrinae libri sex, by the Flemish philosopher Justus Lipsius.