As part of the army of Colonel Gertrudis G. Sánchez, whose forces Arrieta's had joined, Amaro fought against the Zapatistas in Morelos, engaging them at least nineteen times. In one of these engagements, the battle of Jojutla de Juárez, he earned the "Cruz de Segunda Clase," a heroism medal. From 1913 to 1914, he fought the federal troops under the command of Victoriano Huerta, continuing all the while to rise in rank. By 1914 he had risen to the rank of general.
It was under the command of General Sánchez that Amaro developed the reputation of a fierce warrior. It was rumored that he wore an earring and used the battlecry "Here is the man of the pendant earring! Here is the Indian!" He also supposedly emulated the fighting style of the Yaqui people. He also developed the reputation of a harsh disciplinarian who occasionally used his riding crop to mete out corporal punishments to his subordinates. He may have even shot men in his charge or employ for disobeying orders.
In April 1915, he led his troops, known as the "Rayados" ("striped ones"—so-called because the only uniforms Obregón could provide were prison uniforms) to support Obregón's defeat of the villistas in the second Battle of Celaya. Following the battle, Obregón named him Comandante militar ("military commander") of the 5th Division of the Army of the Northwest, and he was charged of ridding Michoacán of villista influence. At the end of 1915, the area under his command was expanded to include Guanajuato and Querétaro.
In 1916, he again fought the zapatistas in Morelos and Guerrero. In 1917, he was placed under the command of Murguía, and led expeditions against the remaining villistas of Durango and Chihuahua.
On September 3, 1921, while chief of operations of the third military zone, Amaro wed Elisa Izaguirre, originally of Morelia, Michoacán. There the couple had two children, Joaquín and Leonor.
He later became commander of the seventh military zone, which comprised Nuevo León. There he put down the July rebellion of Pablo González. When in 1922 political unrest threatened to destabilize Coahuila, Amaro positioned his troops to block the occupation of the state legislature and to protect the governor's palace. In 1923, he was sent to maintain order during Nuevo León's gubernatorial elections. Following a series of violent incidents, Amaro disarmed groups of rural fighters.
Amaro helped plan the assassination of Pancho Villa, who had pledged to support Adolfo de la Huerta if the general rose against Obregón. He later helped free Jesús Salas Barraza, the leader of the group of assassins, from jail.
Amaro's support for the assassination of Villa must not be understood as a betrayal of the Revolution; indeed, Amaro never wavered from his commitment to his interpretation of the Revolution:
I have fought without rest [...] against clericalism, large landowners, the militarism of the ex-Federals, the Spanish, and in general all those that do not contribute to the enrichment of our beloved homeland and the betterment of the working class.
The first, the Law of Discipline, was divided into three sections: General Duties, Corrective Discipline, and Court of Honor. The first three articles of the General Duties defined military duty in terms of "self-sacrifice, loyalty, guardianship, and adherence to the law." The subsequent articles dealt with specific issues. One clarified the officer's duty to maintain order within his ranks; another prohibited soldiers from complaining about orders. One article prohibited servicemembers from interfering in politics. The final articles concerned decorum, and required subordinates to salute and give up their seats to superiors.
The Corrective Discipline section described the circumstances in which soldiers could be arrested for breaking the law, and required that such arrests be recorded in the offender's file.
The Court of Honor section was written for people who committed offenses that threatened the reputation of a unit or of the "dignity of the military." It established a system of courts martial to punish drunkenness, gambling, mismanagement of funds, and negligence. Punishments for those found guilty ranged from transfer to demotion to imprisonment.
The second law, the Law of Retirements and Pensions, allowed servicemembers who had given twenty to thirty-five years of service to retire at will. It also required retirement at a certain age that was dependent on rank. Finally, it provided for pensions for disabled servicemen and their families.
The third law, the Law of Promotions and Rewards, set up two distinct rubrics for promotion: one for peacetime and one for wartime. Peacetime promotions were tied directly to military education. Wartime promotions could be granted for heroic actions such as preventing enemy capture of artillery pieces, and could only be given by high-ranking officers. These promotions had to be approved by higher bodies. These reforms were an effort to end the practice of opportunistic and haphazard promotions which had inflated the number of generals in Mexico's officer corps during the Revolution.
The purpose of the fourth law, the Organic Law, was to organize the armed services. The first section sought to redefine the relationship between generals and the soldiers under them, demanding that all personnel be loyal to the nation and the constitution and take their orders from the President or his designees.
It further delineated the five military branches: high command, combat arms, auxiliary services, special corps, and for the first time, military education establishments, and specified the structures of each. It stratified servicemembers into three classifications: active, reserve, and retired. Another section of the law structured the navy.
Amaro was appointed Secretary of War by President Calles on July 27, 1925. Upon his appointment to the Secretariat, Amaro moved to Rancho de la Hormiga, a 40,468 square kilometer (ten acre) ranch that later became the presidential palace Los Pinos. There his children Guillermo, Manuel, and Elisa were born. He installed recreational facilities such as stables, polo fields, and tennis courts, as well as a military school at the ranch.
In 1927, Generals Francisco Serrano and Arnulfo Gómez conspired with General Eugenio Martínez to seize Calles, Obregón, and Amaro in hopes of igniting a rebellion against the reelection of Obregón. Martínez informed Calles of the plot before it could be enacted, and Serrano and Gómez were caught and executed.
When Obregon was assassinated sixteen days after his 1928 re-election, many generals and other important figures in Mexican politics urged Amaro to run for the office. He always politely declined, stating that he had "never thought to dedicate [his] activities to politics." In February 1929, Amaro was injured during a game of fronton. He took a leave of absence from the Secretariat to seek medical attention at the Mayo Clinic in Rochester, Minnesota. During his three-month convalescence, which left him with a glass eye, Calles assumed the Secretariat, in which capacity he put down the Escobar rebellion against Emilio Portes Gil, who had been appointed interim president in the wake of Obregon's assassination.
Upon his return to Mexico and the Secretariat in May, he found a situation in which Calles was still attempting to control national politics from behind the scenes. Pascual Ortiz Rubio, Portes Gil's successor, was suspicious of Amaro, as was Calles. Calles, purporting to have received information that Amaro was planning on assassinating him or overthrowing Ortiz Rubio, informed the President of the alleged plot. Ortiz Rubio deferred to Calles to take care of the situation, and the Jefe Máximo met with three other cabinet officials, convincing them to resign so as to make it appear that the "cabinet crisis" did not center around Amaro. They agreed, and the following day, Calles, Amaro, and the other three secretarys met at Amaro's estate. There, all four cabinet ministers agreed to resign.
Amaro was succeeded by Calles, who appointed him director of the Heroic Military College.
Despite the Heroic Military College's excellent reputation, by the end of the Revolution, the school was in a state of disrepair. On September 30, 1925, Amaro shut it down for a major overhaul that took ten months. In addition to new facilities, it also boasted a new curriculum that emphasized civic and moral virtues. Admission requirements were put into place, and included letters of recommendation that could vouch for an applicant's moral character.
Amaro's efforts to reform the Mexican military and society extended beyond the realm of military education: he also founded publications that combatted the influence of the Catholic Church and of large landowners in the public consciousness. He had already founded two publications, Acción and El Agrarista, as well as publishing a tract entitled El Gato in the early 1920s. However, 1925 saw a large increase in the number of military journals published in Mexico. Those already in existence, such as the Revista del Ejército y de la Marina (Magazine of the Army and the Navy), took a new editorial stance under the direction of Professor Ignacio Richkarday, who Amaro had appointed editor, to moralize the army. While Revista was aimed at the officer corps, Amaro founded El Soldado, which emphasized the same themes, as a supplement for enlisted men. 1926 saw the founding of two more publications, Revista del Heróico Colegio Militar and Gladiador.
Amaro sought to create a Superior War College along the lines of France's École Supérieure de Guerre to train an elite group of officers. To this end he sent a number of generals to study the militaries and military academies of European and South American states. In particular, he sent Luis Alamillo Flores to study at the French institute, and then to observe military academies in the United States. For two-and-a-half years, Alamillo kept Amaro abreast of his studies through correspondence, and not without reward: in 1931, Amaro informed Alamillo that he would become director of Mexico's Escuela Superior de Guerra. Before he could make good on the offer, however, he resigned from the cabinet.
Amaro led the Heroic Military College from 1931 until 1935, and directed military education for the Secretariat of War from 1931 to 1936.