The Microchannel X-ray Telescope (MXT) is an innovative compact X-ray instrument on board the SVOM astronomical mission dedicated to the study of transient phenomena such as gamma-ray bursts. During 3 weeks, we have tested the MXT flight model at the Panter X-ray test facility under the nominal temperature and vacuum conditions that MXT will undergo in-flight. We collected data at series of characteristic energies probing the entire MXT energy range, from 0.28 keV up to 9 keV, for multiple source positions with the center of the point spread function (PSF) inside and outside the detector field of view (FOV). We stacked the data of the positions with the PSF outside the FOV to obtain a uniformly illuminated matrix and reduced all data sets using a dedicated pipeline. We determined the best spectral performance of MXT using an optimized data processing, especially for the energy calibration and the charge sharing effect induced by the pixel low energy thresholding. Our results demonstrate that MXT is compliant with the instrument requirement regarding the energy resolution (<80 eV at 1.5 keV), the low and high energy threshold, and the accuracy of the energy calibration ($\pm$20 eV). We also determined the charge transfer inefficiency (~$10^{-5}$) of the detector and modeled its evolution with energy prior to the irradiation that MXT will undergo during its in-orbit lifetime. Finally, we measured the relation of the energy resolution as function of the photon energy. We determined an equivalent noise charge of 4.9 $\pm$ 0.2 e- rms for the MXT detection chain and a Fano factor of 0.131 $\pm$ 0.003 in silicon at 208 K, in agreement with previous works. This campaign confirmed the promising scientific performance that MXT will be able to deliver during the mission lifetime.