Measuring distances and areas under forest canopy conditions is often required for a broad range of forest research and management-related activities. While modern technologies, such as handheld mobile laser scanning (MLS), made possible the tridimensional representation of forests with great accuracy, the practical application is still limited by its high costs and challenging data processing. The handheld Global Navigation Satellite System (GNSS) represents the classical alternative, determining the distances and areas based on point coordinates. In this study, we aimed to assess the accuracy of a handheld GNSS, relative to the handheld MLS, in measuring distances and areas under forest canopy conditions. The material consists of 209 ant nests, which were mapped in a mixed-species deciduous forest of North-Eastern Romania. The GNSS- and MLS-based distances among nests were compared using the Bland–Altman plots. The differences in size and shape of the areas described by the nests were analyzed using (i) the shape compactness and (ii) the form factor of the convex polygons. In general, the GNSS-based distances were shorter compared with those based on MLS. However, for most cases, the intervals of agreement between the two instruments were within the limits of GNSS accuracy (i.e., ±10 m). The largest mean differences occurred when nests were in dense canopy conditions and on rugged terrain. The GNSS-based area of the convex polygons was smaller in most cases, but no significant correlation between the size of the area and the size of the relative difference was found. Furthermore, both the shape compactness and the form factor of the polygons were also smaller for the GNSS-based method compared with the MLS-based method, with differences up to 10%. In conclusion, measurements recorded by GNSS were less accurate, and under certain forest conditions (dense canopies, rugged terrain), large systematic errors can occur and therefore limit its use.