Instead, having moved to Faro in the decade of 1770, he would eventually enlist in the Portuguese Army, as a Pé de Castelo (Castle Guard) in 1793, as a gunner, at the age of 29.

In 1795 and 1796, he was part of the artillery complement of the Nau Príncipe da Beira, the flagship of a fleet escorting commercial ships to Salvador, in Brazil.

Upon returning to Lisbon, he was promoted to captain in the Light Troops Legion, an experimental unit of the Portuguese Army, eventually becoming the aide-de-camp to General Marquis of Alorna.

On the occasion of the first French Invasion of Portugal, in November 1807, Carlos Frederico Lecor is credited with having spotted the invading army, commanded by Junot, north of Abrantes, and having personally informed the Prince-Regent, future King John VI.

In June, 1815, he was promoted to lieutenant general and appointed commander of the Prince's Royal Voluntary Division (Divisão de Voluntário Reais do Príncipe) a unit to be sent for service in Brazil, made up mostly of peninsular veterans.

During this war, he succeeded in defending Montevideo against an Argentine-Uruguayan siege, but when Uruguay became independent in the peace treaty, he had to return to Brazil.