In Worms Forts: Under Siege, the gameplay follows a similar structure to the main Worms series games, except players can construct fortifications that can strengthen the defensive potential of either team. Each player takes turns to construct fortifications and/or make an attack. Players can build a variety of these fortifications, which in return offer special bonuses that improve the defense of their own teams. Forts have to be constructed so that they are connected to a singular large fortification called the "Stronghold". A variety of forts are progressively unlocked based on players' performance on expanding fortifications across the land from the Stronghold via a network-like system. As the game progresses, the player can construct increasingly larger forts that are capable of deploying stronger weapons, or construct special buildings that provide special gameplay benefits, such as the generation of collectible health crates or weapon crates. Players can fire from special forts designed to deploy stronger siege weapons, compared to basic weapons such as the grenade or bazooka.
At the start of each game, each player starts with a "Stronghold", a large fortification with high health. Weapons are used to destroy buildings and their links. Isolated forts that have lost all links to the Stronghold are immediately destroyed. Destroying the Stronghold immediately destroys all forts and subsequently forces the associated team to forfeit. The player wins by defeating the opposing team(s), achieved by either killing all their worms or destroying their strongholds.