Cog Headquarters are areas that are permanently controlled by Cogs. These areas are usually more difficult and dangerous compared to other locations in Toontown. Toons will also be assigned ToonTasks related to the four Cog Headquarters as they progress through the game.
- Main article: Sellbot Headquarters
Sellbot Headquarters (also known as SBHQ or Sellbot HQ) is a Cog HQ where the Sellbots reside in. It was released on May 21, 2014. The theme is an industrial wasteland. The facilities in Sellbot Headquarters are the Sellbot Factory and Sellbot Towers. Cogs ranging from Cold Callers to Two-Faces can be found wandering around the courtyard. Cogs in the courtyard can range from level four to level six. The boss of the Sellbots is the Vice President. This is the first Cog HQ that Toons face.
- Main article: Cashbot Headquarters
Cashbot Headquarters (also known as CBHQ or Cashbot HQ) is a Cog HQ where the Cashbots reside in. It was released on June 5, 2014. The theme is a gigantic train station. The facilities in Cashbot Headquarters are three Cashbot Mints and the Cashbot Vault. Cogs ranging from Tightwads to Money Bags are in the train yard. The boss of the Cashbots is the Chief Financial Officer. This is the second Cog HQ that Toons face.
- Main article: Lawbot Headquarters
Lawbot Headquarters (also known as LBHQ or Lawbot HQ) is a Cog HQ where the Lawbots reside in. It was released on June 26, 2014. Before the tunnel of Lawbot Headquarters finished construction, there were secret ways of getting there known as Doctor Surlee's teleportation bypasses. The theme is a clean marble plaza in a city. The facilities in Lawbot Headquarters are the District Attorney's Office and the Lawbot Courthouse. Cogs ranging from Ambulance Chasers to Spin Doctors are in the courtyard. The boss of the Lawbots is the Chief Justice. This is the third Cog HQ that Toons face.
- Main article: Bossbot Headquarters
Bossbot Headquarters (also known as BBHQ or Bossbot HQ) is a Cog HQ where the Bossbots reside in. It was relased on May 3, 2015. Before the tunnel of Bossbot Headquarters finished construction, the only way to get there was to use the Resistance Salute in a specific area at Chip 'n Dale's MiniGolf. The theme is a huge country club with a terrifying atmosphere that would spur sadness onto any onlooker. The facilities in Bossbot Headquarters are three Cog Golf Courses, the Bossbot Clubhouse, and the Executive Office Tower. Cogs ranging from Micromanagers to Head Hunters are found in the courtyard. The boss of the Bossbots is the Chief Executive Officer. This is the fourth and last Cog HQ that Toons face.