The Maledictors follow a standard organisation structure as it is laid down in the Codex Astartes. The chapter is comprised of ten companies that each maintain roughly 100 marines. Each company is led by a Captain who is often joined in battle by specialists from the Reclusium or the Apothecarion. The marines within each company are organised into ten squads that specialise in one of three roles defined by the Codex as Tactical, Assault and Devastator squads. The exceptions to this structure are notably the 1st Company, where the marines will form different squads depending on how they are fielded, and the 10th Company, where the Scout Squads can vary greatly in size depending on the level of recruitment at that time.

The chapter Headquarters includes many specialist and dedicated marines who work to ensure the chapter is correctly run, supplied with equipment and to heal those injured in battle. The chaplains can also be found here, ensuring that the Maledictors stay true to their beliefs and spurring them on in the heat of battle.

The Battle Companies are the main fighting strength of the chapter and comprise of the most experienced and stoic warriors in the Maledictors. Each company is fully capable of fighting alone or alongside squads from the rest of the chapter. Rarely will a single company be dispatched to a warzone, instead a force led by a Battle Captain will be created from elements from across the chapter. The 1st Company Veterans are often fielded in this way, lending their superior skills to where they can best be utilised.