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Abstract Free-electron-lasers fill a critical gap in the space of THz-sources as they can reach high average and peak powers with spectral tunability. Using a waveguide in a THz FEL significantly increases the coupling between the relativistic electrons and electromagnetic field enabling large amounts of radiation to be generated in a single passage of electrons through the undulator. In addition to transversely confining the radiation, the dispersive properties of the waveguide critically affect the velocity and slippage of the radiation pulse which determine the central frequency and bandwidth of the generated radiation. In this paper, we characterize the spectral properties of a compact waveguide THz FEL including simultaneous lasing at two different frequencies and demonstrating tuning of the radiation wavelength in the high frequency branch by varying the beam energy and ensuring that the electrons injected into the undulator are prebunched on the scale of the resonant radiation wavelength.