We report a novel injection moulding technique for fabrication of complex multi-layer microfluidic structures, allowing one-step robust integration of functional components with microfluidic channels, and fabrication of elastomeric microfluidic valves. This technique simplifies multi-layer microfluidic device fabrication, while significantly increasing device functionality. We demonstrate functional component integration through robust encapsulation of porous polyester membranes, in the context of an in vitro research platform intended to facilitate Blood Brain Barrier (BBB) research. We also demonstrate the fabrication of normally-closed, pneumatically actuated elastomer valves, integrated using the same one-step process. These valves are demonstrated in the context of variable flow resistors used to modulate flow in a pressure driven system.