This also allowed a player to take over a single territory on an enemy-colonized planet and attempt to build it up. Over time a single colonization attempt would take over an entire planet. As the population grew and started to reach the maximum for any one territory, they would naturally migrate out of a territory into surrounding ones. Territories had a natural population limit based on their ecological fitness for the player's species.

Larger planets and moons had multiple 'territories' in the higher skill level settings. These attributes impacted the race's rate of scientific discoveries, building speed, population growth, and on-planet combat effectiveness, respectively. Options included which atmosphere type they breathed (oxygen, nitrogen, carbon, or hydrogen), temperature range and tolerance, and four percentile-rated attributes: curiosity, efficiency, reproduction, and aggression. Races could be customized by players at the start of the game. Unlike most other 4X games, Pax had much more complex solar systems, including moving planets, their moons, and a habitable temperature zone that varied depending on the star and the race's preferences. Once captured, the worlds could be upgraded to provide materials, ships, and improve their defensive capabilities.

Like most 4X games, Pax Imperia's basic gameplay involved building spaceships and flying to other worlds in order to take them over. In the Beginner skill level, the player also starts with several ships, visible in the system. The player has started with their home world in Cygnus, the star with the crown. The Pax Imperia Universe window, at the start of a game.

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