We developed a multispectral-augmented endoscopic prototype which increases the common number of bands under analysis, allowing exploration in the visible and near infrared range (400–1000 nm). The prototype combines endoscopy with spectroscopy using white light (WL) or Narrow Band Imaging light (NBI) endoscope and two multispectral cameras connected to a twin-cam splitter. The splitter is then connected to an optical fiber and introduced in the endoscope instrument channel. In this work, we introduce a spectral calibration and an axial displacement correction function to register both modalities. The former is based on a multi-linear transformation of multispectral bands and its performance is assessed using a Digital SG ColorChecker® pattern to report an RMSE of 6.78%. The latter relates the insertion depth of the fiberscope with the required geometric transformation. The performance was assessed using a chessboard pattern and its corner coordinates as ground truth. The mean RMSE error for the registration using our method was 2.3 ± 0.7 pixels, whereas the RMSE error using a frame by frame homographic registration was 1.2 ± 0.4 pixels. Finally, the technique was tested on mouth exploration samples to simulate in-vivo acquisition and display complete spectra for single points of analysis. The results reveal that our method provides similar performance when compared to a homographic transformation which would be impossible to perform in-vivo.