Described herein are methods and systems for manufacturing composite stringers using independently movable pallets with independent vacuum controls. Specifically, a stringer forming system comprises a base plate and a plurality of sets of pallets (e.g., two or more sets of pallets), slidably coupled to the base plate and forming an adjustable cavity. Each pallet comprises a primary vacuum zone, fluidly connected to a separate vacuum port. The system allows for independent application of a reduced pressure to the primary vacuum zone of each pallet. For example, a reduced pressure is applied only to pallets that are already covered with a composite layup and to pallets that are being covered. Any pallets that are exposed are kept at an ambient pressure and decoupled from a vacuum source, thereby reducing the vacuum leakage through the overall system. As the composite layup is being formed over new pallets, these new pallets are subjected to the reduced pressure.