The Confederate military, also known as the Separatist armed forces or CIS armed forces, represented the military might of the Confederacy of Independent Systems. Its structure included various divisions, most notably the Separatist Droid Army and the Confederacy naval forces. The Droid Army consisted of components such as the Techno Union Droid Army, the Trade Federation military, the Geonosian droid army, the IG-series battle droid army, the Retail Caucus droid army, and the forces of the InterGalactic Banking Clan, the Corporate Alliance, and the Commerce Guild. In addition, individual planets, star systems, and sectors contributed their own local military contingents.

Thirteen years prior to the decline of the Republic, the Trade Federation gained permission to maintain a military force composed of B1-series battle droids for the purpose of safeguarding valuable cargo from acts of piracy. The initial large-scale employment of the Trade Federation's army took place during the blockade and subsequent invasion targeting Naboo. In this conflict, the army engaged both the Royal Security Forces and the Gungan Grand Army. The Trade Federation fleet was deployed to establish a blockade around the planet. Nevertheless, the Federation military ultimately suffered defeat when the young Force-sensitive Anakin Skywalker successfully destroyed the Vuutun Palaa, which led to the deactivation of the battle droids.
Various other powerful organizations, including the Techno Union, possessed their own military forces for the protection of their vested interests. As the Separatist Crisis unfolded, the Techno Union, the Trade Federation, and other similar entities committed their respective armies to the command of Count Dooku and the newly forming Confederacy of Independent Systems. These forces collectively established the foundation for the military. The Retail Caucus also pledged their droid army before the Battle of Christophsis. In the years leading up to the Clone Wars, the Confederacy had secretly been developing and training command personnel.
Following a meeting held on Geonosis involving Dooku and his allies, the Republic gained knowledge that the Confederacy intended to utilize the shipment and its army to coerce the Republic into meeting their demands. After Jedi Master Obi-Wan Kenobi was taken prisoner, the Republic's Supreme Chancellor Palpatine received emergency powers from the Galactic Senate to initiate the creation of a Grand Army of the Republic, employing an army that had been commissioned by Jedi Master Sifo-Dyas. The Separatist Droid Army and the Republic's Grand Army engaged in combat on Geonosis during the initial engagement of the Clone Wars.

Despite suffering a defeat, the Confederacy managed to secure control over the primary hyperspace lanes, effectively isolating the Republic from the majority of its military personnel. The military would persist as a formidable and effective fighting force against the Republic.
Even though the Republic achieved more victories than defeats, the droid armies under the leadership of Grievous secured numerous triumphs against the Republic, including the capture of Eeth Koth and the bombing of Coruscant's central power distribution grid. One of Grievous's most audacious offensives occurred near the war's conclusion when he initiated an attack on Coruscant and attempted to flee with the Supreme Chancellor. However, this endeavor failed when Kenobi and Skywalker eliminated Dooku and successfully rescued the Chancellor. In addition to Dooku's demise, the Separatists incurred the loss of one-third of the fleet they had deployed during the Battle of Coruscant.
Following Dooku's death, Grievous assumed the role of the new Head of State for the Confederacy. Nevertheless, his tenure was short-lived, concluding abruptly when Kenobi located and destroyed him on Utapau. Subsequently, the military came under the command of the Council. However, their authority was terminated when Lord Sidious's new apprentice, Darth Vader eliminated them on Mustafar. Vader also transmitted a master control signal that deactivated a significant portion of the Separatist military's droid forces. The elimination of the Separatists and the Great Jedi Purge enabled Palpatine to establish his Galactic Empire with himself as Emperor.
Despite the disbandment of the Confederacy, its influence persisted in the form of Separatist holdouts. Stormtroopers of the Empire were assigned the task of destroying any surviving battle droids upon discovery. During the Imperial Era, at least three anti-Imperial insurgent groups, Cham Syndulla's Free Ryloth Movement, Berch Teller's rebel cell and Nevil Cygni utilized Separatist equipment.

In 2 BBY, the former Clone Captain Rex and members of the Spectres rebel cell encountered the super tactical droid general Kalani and his garrison of battle droids on Agamar during a salvage mission to obtain proton bombs from a derelict Separatist supply ship. Kalani had overrode the command signal on Agamar, believing it to be a Republic trick. Determined to end the Clone Wars on his terms, Kalani forced Rex and the Spectres to take part in a war game. The Jedi Padawan Ezra Bridger convinced Kalani and Rex to put aside differences and make peace. The two sides then joined forces to escape an Imperial attack on Agamar.
The future New Republic and Resistance starfighter pilot Temmin Wexley also rebuilt and befriended a heavily-modified B1 battle droid named Mister Bones. Mister Bones fought during the Galactic Civil War and met his end at the Battle of Jakku.

As Head of State of the Confederacy and leader of the Separatist Senate, Dooku possessed the most authority over the Confederacy's military operations and strategies, and he served as a member of the Separatist high command. The Confederacy's most accomplished general was the Kaleesh cyborg Grievous, who held the position of Supreme Martial Commander of the Separatist Droid Armies. Together, Dooku and Grievous influenced the Confederacy's military and propelled it forward.
Beneath Grievous and Dooku were several high-ranking officers, including Supreme Leader Asajj Ventress, General Kleeve, Duke Solha, and Colonel Coburn Sear. Members of the Separatist Council, such as Viceroy of the Trade Federation Nute Gunray, Emir Wat Tambor, High Admiral Reaves, and Archduke Poggle the Lesser, were also known to personally oversee various military operations.
While primarily consisting of droid forces, the Confederacy's military also encompassed the local armed forces of the planets under its dominion. The Umbaran Militia, Zygerrian royal guards, several Kage Warriors, and Geonosians from the Stalgasin hive were among those who provided leaders and additional support.

The droid army was the largest military force assembled in its era, reportedly exceeding the Republic clone army by a ratio of one hundred to one. The Separatist Droid Army was composed of the military forces of several major corporations, including the Trade Federation Droid Army, the Techno Union Droid Army, the Retail Caucus's private droid army, the army of the Commerce Guild, and the army of the Corporate Alliance. The Separatist ranks also included a limited number of organic soldiers; however, leaders such as Count Dooku emphasized that these were volunteers rather than cloned soldiers who had been forced into service.

The Confederacy of Independent Systems Navy engaged in early combat during the Clone Wars at the Battle of Christophsis, where Admiral Trench blockaded the planet and resisted Republic forces until his flagship, the Invincible, was destroyed. One vessel in the navy, the Subjugator-class heavy cruiser Malevolence, terrorized Republic convoys early in the war and was initially regarded as a "mystery weapon." It was eventually discovered that the Malevolence was equipped with two mega-ion cannons that could disable enemy vessels with a single shot. The Malevolence was destroyed during the Battle of the Kaliida Nebula.
The Separatist navy primarily consisted of starships utilized by organizations such as the Trade Federation and the InterGalactic Banking Clan. The capital ships were also supported by starfighter forces, primarily composed of Vulture-class droid star fighters and droid tri-fighters.
CIS Special Operations served as the special forces arm of the CIS military.