The dental biofilm plays a central role in the caries process, as tooth minerals will deteriorate or maintain their integrity based on the biofilm activity. For example, the acid production by the biofilm microbiome upon exposure to fermentable sugars will drive mineral dissolution; the concentration of ionic species such as calcium, phosphate and fluoride ions present in the fluid of the biofilm will determine mineral precipitation or dissolution. Studies focusing on properties of cariogenic biofilms beyond microbial counts (e.g. biofilm organic and inorganic composition and structure) have offered important information for the understanding of the dental caries process and the effect of different anticaries approaches. Here we describe preclinical models (in situ and ex vivo studies) that have been used to study biofilms associated with dental caries and detail the methodologies that can be used for a deeper understanding of these biofilms’ dynamics.