At the start of the adventure the player has two small ships but as progress is made the fleet might grow and it is also possible for the player to customize his fleet. The player can get ship upgrades either from an event or from being victorious in battle.
Some events lead to combat with other fleets of the galaxy. The battles of Flotilla are simultaneous turn-based, meaning that the player moves at the same time as his enemy. The combat consists of two phases: the orders phase and the action phase. In the order phase the player gives orders to each of his ships. Three different orders are available: the attack move which allows the ship to move and fire at the same time, the flank move which allows the ship to move to a better position without firing, and the focus fire which allows the ship to fire with an increased fire rate but only at a short move distance.
Once an order is selected, it's executed in four steps. First the player selects the horizontal movement and after that the vertical. The player also has to choose in what angle the ship should face and which enemy ship should be the primary target. For more advanced gameplay, the player can choose to turn on the manual mode which allows him to control how the ships will yaw, pitch and roll.
After all ships have got their orders, the player ends the turn and the action phase is launched. Here the player can only watch as the ships carry out their orders. There's no interactivity in the action phase (besides camera movement) so there's no way back once an order has been assigned.
Ships have heavy armour which is able to deflect most projectiles. However each ship has two weak spots, the rear and the bottom. Therefore flanking is a very important tactic since it allows the player to hit the rear side of the enemy ships. The vertical movement is also important since it allows the player to attack from below. The ships gain combat experience for each battle and this leads to the ship's veterancy level increasing. A ship with high veterancy is more effective in combat since it does more damage and has better armour performance.
In addition to the adventure mode described above, the game also has a skirmish mode which allows the player to jump straight into battle. The skirmish mode can be played both against another player or against the AI. In the skirmish mode it is possible to choose from any ship available in the game.