In Cone Beam CT (CBCT) systems, each acquisition is carried out with a stationary bed. Therefore, the field of view is limited by the size of the detector. To overcome this limitation, it is common to perform successive acquisitions for different bed positions, which are subsequently combined to increase the field of view in the longitudinal direction. To avoid the appearance of double edges in the resulting volume, it is necessary to calculate the exact bed displacement, which has traditionally been obtained by prior geometric calibrations with calibration phantoms. This implies that the calibration must be repeated periodically to adapt to any changes that the equipment may undergo. As an alternative, in this work we propose the use of an automatic calibration algorithm capable of obtaining the misalignment parameters in real time, allowing to obtain multi-bed images in small and regular animal CBCT systems without the need of a previous calibration.