The first armed conflict broke out in 949, when 56 monks from Tōdai-ji staged a protest at the residence of a Kyoto official, over an appointment that displeased them.
Taira no Kiyomori sent generous gifts of rice and silk to Enryaku-ji, ensuring they would not help his enemies, the Minamoto, who had allied themselves with the monks of Mii-dera.
The warrior monks stood their ground with bow and arrow, naginata, sword and dagger, but were ultimately defeated.
Their political influence grew stronger through peaceful means, and the warrior monks played only very minor roles in the wars of the 13th and 14th centuries.
The Ashikaga shogunate took power shortly afterwards, and supported Zen over the other Buddhist sects, drawing the ire of the warrior monks.
Their growing power base was eventually to attract the attention of warlords like Oda Nobunaga and Tokugawa Ieyasu, who recognized their opposition to samurai rule, their determination, their strength, and their numbers.
As Oda Nobunaga rose to power at the end of the 1560s, the monks of Enryaku-ji regained their military might, and fought a number of skirmishes in the streets of Kyoto against a new rival sect, Nichiren Buddhism.
They eventually burned all of Kyoto's Nichiren temples to the ground, and then sought allies among the local lords (daimyō).
Beginning on September 29, 1571, Nobunaga's army of 30,000 led the Siege of Mount Hiei, destroying Enryaku-ji and massacring thousands.
In the summer of 1574, with the help of former pirate Kuki Yoshitaka, Nobunaga essentially blockaded the Ikkō fortresses and starved them into submission.
In the 1580s and 1590s, various factions of warrior monks sided with either Tokugawa Ieyasu or his rival Toyotomi Hideyoshi, fighting in a number of battles and skirmishes.
The naginata is the weapon most often associated with them, though in legend as well as history many warrior monks are known to have been proficient with everything from yari, yumi, tachi, and tantō.
Warrior monks would often fold and tie the white headcowl to cover more of their head, or would substitute a hachimaki headband.
The Ikkō-ikki monks of the 16th century, due largely to their origins as countryside mobs, were far more varied in their armor and armament.
Naginata remained very common, along with a variety of swords and daggers, and a limited number of arquebuses (with the Saika Ikki being a notable exception, as they are mainly composed of musketeers and gunsmiths as per Suzuki Magoichi's standard of having an all-musketeer army).
Finally, while not truly armor nor armament, a very common item wielded by the mobs of Ikkō-ikki monk warriors was a banner with a Buddhist slogan written upon it.