A three-dimensional survey of natural caves is often a difficult task due to the roughness of the investigated area and the problems of accessibility. Traditional adopted techniques allow a simplified acquisition of the topography of caves characterized by an oversimplification of the geometry. Nowadays, the advent of LiDAR and Structure from Motion applications eased three-dimensional surveys in different environments. In this paper, we present a comparison between other three-dimensional survey systems, namely a Terrestrial Laser Scanner, a SLAM-based portable instrument, and a commercial photo camera, to test their possible deployment in natural caves survey. We presented a comparative test carried out in a tunnel stretch to calibrate the instrumentation on a benchmark site. The choice of the site is motivated by its regular geometry and easy accessibility. According to the result obtained in the calibration site, we presented a methodology, based on the Structure from Motion approach that resulted in the best compromise among accuracy, feasibility, and cost-effectiveness, that could be adopted for the three-dimensional survey of complex natural caves using a sequence of images and the structure from motion algorithm. The methods consider two different approaches to obtain a low resolution complete three-dimensional model of the cave and ultra-detailed models of most peculiar cave morphological elements. The proposed system was tested in the Gazzano Cave (Piemonte region, Northwestern Italy). The obtained result is a three-dimensional model of the cave at low resolution due to the site’s extension and the remarkable amount of data. Additionally, a peculiar speleothem, i.e., a stalagmite, in the cave was surveyed at high resolution to test the proposed high-resolution approach on a single object. The benchmark and the cave trials allowed a better definition of the instrumentation choice for underground surveys regarding accuracy and feasibility.