Interactions between amyloid proteins represent the cornerstone of various pathogenic pathways, including prion conversion and co-development of distinct kinds of systemic amyloidosis. Various experimental methodologies provide insights into the effects of such cross-interactions on amyloid self-assembly, which range from acceleration to complete inhibition. Here, we present a comprehensive review of experimental methods most commonly used to study amyloid cross-interactions both in vitro and in vivo, such as fluorescence-based techniques, high-resolution imaging, and spectroscopic methods. Although each method provides distinct information on amyloid interactions, we highlight that no method can fully capture the complexity of this process. In order to achieve an exhaustive portrayal, it is necessary to employ a hybrid strategy combining different experimental techniques. A core set of fluorescence methods (e.g., thioflavin T) and high-resolution imaging techniques (e.g., atomic force microscopy or Cryo-EM) are required to verify the lack of self-assembly or alterations in fibril morphology. At the same time, immuno-electron microscopy, mass spectrometry, or solid-state NMR can confirm the presence of heterotypic fibrils.