The transformation of plants into foodstuffs can be regarded as a form of cultural expression, and the culinary practices that accompany this transformation have the capacity to serve as indicators of social and cultural identities within the archaeological record. The COMAL project (2023-2025) sought to employ innovative methodologies to ascertain the plants consumed by the ancient Maya, who inhabited present-day Mexico and Guatemala, during the Classic period (AD 250-900) and to determine the methods by which these plants were processed. The objective of this study was to examine the microstructure of remains in order to reconstruct the transformation processes that could potentially lead to the reconstruction of ancient recipes. This approach had never before been attempted on materials from this region. Two sets of data were considered. The first are amorphous carbonized objects (ACOs), macrobotanical remains collected by flotation that may be leftovers from complex, multi-ingredient foods. The second set of data are microremains (i.e. biomolecules), which are expected to be found on the active surfaces of tools (e.g. grinding stones and ceramics) used to prepare and serve food. In both cases, a reference collection of individual plants and more complex foods had to be prepared in a laboratory setting. Different types of imaging and chemoprofiling analyses were then performed. Then, the archaeological samples were tested and compared to the reference collection. These reference collections, specifically the identification of features and markers that remain after carbonization, are invaluable for future analyses. This research highlights the potential of using other lines of evidence to reconstruct ancient diets. This makes it particularly useful for archaeologists working in the Maya region and across the Americas. Furthermore, the data will be important for current Maya populations in Mexico and Guatemala who have maintained their traditions despite the Spanish conquest in the 16th century.