Linear morphometrics is the most widely applied technique to study the variation of the conch morphology in ammonoids and other ectocochleate cephalopods. However, because this method frequently relies upon a few linear measurements, it lacks the explanatory power to accurately characterize the shape of the whorl cross-section, which is instead discussed solely in descriptive terms, e.g., elliptical, triangular, or subquadrate. Here, we introduce a landmark-based geometric morphometric approach to study ammonoid whorl cross-sections, derived from the regularly used morphometric parameters in cephalopods. This new technique uses virtual modelling to generate semilandmark configurations and virtual models of whorl cross-sections. We applied it to study 50 ammonoid specimens belonging to 48 genera exhibiting a wide range of morphologies and ages. Results indicate that this new method is appropriate to describe the shape of ammonoid whorl cross-sections, allowing us to construct a morphospace showing several biological patterns (e.g., clustering and homeomorphy), and complex morphological transformations that, in some cases, correlate with evolutionary tendencies described by previous authors. Further, this technique can be used to generate the basic segment required for the elaboration of the virtual models employed in hydrostatic and hydrodynamic studies.