Multispectral measurement and analysis have proven to be useful to detect and monitor gastric pathologies at early stages. We developed a multispectral-augmented endoscopic prototype which allows exploration in the visible and near infrared range (400-1000 nm), increasing the common number of bands under analysis. The prototype comprises a fiberscope connected to two multispectral snapshot cameras which is inserted through the instrument channel of a commercial endoscope. However, due to aseptic practices, the system must be sterilized between exams, forcing physicians to remove and reintroduce it on each examination and leading to different relative positions between modalities. In the present work, we introduce an axial displacement correction function for dual-channel registration (i.e., RGB and multispectral) based on the insertion depth of the fiberscope. The performance was assessed using a chessboard pattern and its corner coordinates as ground truth. The mean RMSE error of the control points after 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. In addition, the technique was tested on mouth exploration samples to simulate in-vivo acquisition. The results reveal that our method provides similar results when compared to a homographic transformation which would be impossible to perform in-vivo.