He was married to Mary Ann Coventry, a Scottish woman who was the widow of John Borthwick Gilchrist, linguist and surgeon to the East India Company.

He entered Napoleon's army and served with distinction in several campaigns, including those in the Neapolitan kingdom: first under Joseph Bonaparte, and later under Joachim Murat.

When news of the fall of Napoleon (1814) reached Italy, Pepe and several other generals tried, without success, to force Murat to grant a constitution as the only means of saving the kingdom from foreign invasion and the return of the Bourbons.

[1] Meanwhile, the king, who had no intention of respecting the constitution, went to the Congress of Laibach to confer with the sovereigns of the holy alliance assembled there, leaving his son as regent.

Pepe then spent several years in England, France and other countries, publishing a number of books and pamphlets of a political character and keeping up his connection with the Carbonari.

Pepe, after hesitating between his desire to fight for Italy and his oath to the king, resigned his commission in the Neapolitan service and crossed the Po with 2,000 volunteers to take part in the campaign.