Inca battalions were integrated by permanent staff (generals and officers) and non-permanent personnel composed by drafted hatun runas (common men) who would be serving their military mita (comparable to a mandatory military service). Once the mita was fulfilled, each hatun runa would return to its respective ayllu (community).

Each battalion was made up by a single ethnic group, the whole group being directed by the Curaca (war lord) of the group. In the event the Curaca would fall in battle, a deputy Curaca was appointed within the same ethnic group. In order to prevent rebellions and to promote performance in battle, each ethnic group was divided in two battalions, each one under the command of a general (and both under the command of the Curaca) who would compete against his counterpart in exhibiting performance in the battlefield and thus increasing his chances of promotion. This "duality" concept is widely spread across the Andean world, and represents the two Inca dynasties: Hanan and Hurin.

Since the government of Inca Tupac Yupanqui, a specialized elite of soldiers was appointed for the safekeeping of the Sapa Inca (The One and Only Inca) during parades, travel or campaigns. These bodyguards originated primarily in Cuzco, even though with time other ethnicities were accepted in this elite group. This imperial guard, all of them belonging to the nobility, reached a size of 10,000.

All members of the Inca army were between 25 and 50 years old. All of the empire's citizens had to perform either military or community service. One of every 50 men over 25 years old (legal age in the Inca Empire) would be chosen for military service. For noblemen, this was an honor and a duty, for common men, this was a means of social promotion. Per the duality concept, one of every 50 young women were selected to serve in the Temple of the Virgins of the Sun.

After a certain period of time (usually 6 or 7 years), the military service was considered to be fulfilled for common men. However, professional officers were permanent soldiers and paid by the state. This military caste enjoyed several privileges. Food and housing costs were covered by the state, as well as clothing and several other gifts such as coca, jewelry, and wives.

Runas (common men) from the coastal region, unlike people from the highlands, were not compelled to serve in the army. This is probably explained by their lack of adaptation to the harsh climate conditions of the highlands, where most wars took place.

Inca armies were well-disciplined and organized; troops used to maintain silence and only break it by yelling and singing just before attacks, in order to intimidate the opposing force. It is worth noting that the army units would march in the company of an important number of women, mostly relatives of the soldiers. Women would take care of cooking and repairing the soldier's clothes, and after battles would attend the wounded and help bury the dead. Inca armies would not fight at night for religious reasons. A group of priests would also be attached to the army units, in order to pray, make sacrifices, and try to weaken the opposing force by casting spells before and during battle. Weapons and other equipment were transported by llamas.

There was a reward system in place for distinguished services. Soldiers displaying bravery beyond expectations were rewarded with medals, metal objects, and uniforms.

Once a battle was over, enemy leaders would only be executed if they refused to accept the sovereignty of the Sapa Inca. The majority of conquered nations would be absorbed into the Empire. Conquered nations were forced to adopt Quechua as a primary language and to adopt Inca social customs. Inca government officials would perform a careful study of the conquered zone to ensure the achievement of these objectives.