He continued to defend Tamaulipas through its national guard until 1854, the year he was elected as a lieutenant colonel due to his efforts in protecting local territories from the Texan military and the native tribes.

[4] In 1854, Hinojosa adhered to the Plan of Ayutla against Antonio Lopez de Santa Anna joining the national guard of Tamaulipas, and having ascended to the position of colonel in the triumph of the revolution, became a permanent formal member of the military.

After the coup by Felix Zuloaga he remained loyal to the government of Benito Juarez and fought with the liberal band during the Reform War, fighting in the Batalla de Lomas Largas, in the siege of Monterrey, where he was made a prisoner by the conservatives.

Hinojosa thereafter fulfilled the office of federal delegate until December 22, 1861, when president Benito Juarez named him Secretary of War and Navy.

He participated in the defense of the city of Puebla de Zaragoza which was besieged by the French troops and had to surrender in 1863, falling prisoner to the invaders.

Hinojosa was then given the leadership of the republican troops in Tamaulipas and together with Mariano Escobedo they victoriously attacked the imperialist garrison in the port of Matamoros.

In 1871 he joined the uprising in favor of Porfirio Díaz pursuing the Plan of La Noria against Benito Juarez, in which he was defeated and taken prisoner in Saltillo.

Hinojosa remained in this post until August 14, 1878 at which time he turned over the governorship to his constitutionally elected successor Angel Trias Ochoa.