A method automatically controls stores for a processing line for containers pre-dosed with fluid products. The identifying code for each container is determined and then checked whether the container is necessary for production orders received. The container is introduced into a first store and the quantity and identifying codes of the containers in the first store are recorded. Production orders are checked for products yet to be started. The containers are picked up and sent towards a first manipulation station and at least one production order of a product is processed and the containers are sent towards different stations. Quality control inspection is conducted and if the product is compliant, introduced into a second store. Containers with non-compliant product are introduced into a control line. The quantity of containers in the second store is recorded and the containers are sent towards a packaging station to fulfill production orders.