Microwave chemical processing system having a microwave plasma reactor, and a multi-stage gas-solid separation system are disclosed. The microwave energy source has a waveguide, a reaction zone, and an inlet configured to receive the input material, and the input material is converted into separated components. The separated components include hydrogen gas and carbon particles. The multi-stage gas-solid separation system has a first cyclone separator to filter the carbon particles from the separated components, and a back-pulse filter system coupled to the output of the first cycle separator to filter the carbon particles from the output from the first cyclone separator.