Norton de Matos' return to Portugal coincided with Portugal's conversion into a republic. He was prepared to serve the new regime, and he soon became the chief of staff of the 5th military division. In 1912 he gained the post of governor - general of Angola. His leadership was considered instrumental in protecting the Portuguese colony from foreign powers such as England, Germany and France.

Norton de Matos was recalled to Portugal in 1915 due to a new political situation that arose in Portugal during the First World War and named Minister of War. In this capacity, he was responsible for organizing the Portuguese intervention on the Western Front.

In 1917, Norton de Matos exiled himself to London after disagreements with the new republic. He later returned and became the Portuguese delegate to the Paris Peace Conference, which led to the Treaty of Versailles. Later he returned to Angola as High Commissioner of the Republic, from 1921 to 1923, before becoming Portuguese ambassador to the United Kingdom from 1923 to 1926. In 1929 he was elected a Grand Master of the Masons in Portugal.

Norton de Matos returned to teaching, accepting a position as professor at the Instituto Superior Técnico, but was dismissed from his chair. He then became a leading opposition figure against the Salazar regime. In 1943, he was named to the National Council of Movement of National Antifascist Unity, or MUNAF, and on his 81st birthday, he was named the opposition candidate for President in the rigged election of 1949, under the dictatorial Estado Novo regime, while demanding freedom to advertise his message and the close inspection of votes. The regime refused these demands, and Norton de Matos withdrew from the election on February 12, 1949.

Norton de Matos continued to lead a democratic opposition movement centered in the city of Oporto. He died in the city of his birth in 1955.