The eggs of Echinococcus multilocularis, the infectious stage, are spread into the environment through wild and domestic carnivore faeces. The spatial location of the faeces containing infective E. multilocularis eggs is a key parameter for studying areas of exposure and understanding the transmission processes to the intermediate hosts and humans. Echinococcus multilocularis faecal prevalence is often assessed by detecting E. multilocularis DNA, not necessarily eggs. This work aimed to determine the percentage of faeces containing E. multilocularis eggs in a rural town and its surroundings and whether this level of precision is relevant in assessing exposure to E. multilocularis. For this purpose, we developed a combined molecular and microscopic approach to investigate the E. multilocularis exposure of potential hosts in the environment from field-collected carnivore faeces. Carnivore defecation patterns were then spatialized to study the spatial distribution of E. multilocularis. Faeces were screened for E. multilocularis DNA using a specific real-time quantitative PCR (qPCR). Echinococcus multilocularis eggs were morphologically identified from E. multilocularis-specific qPCR-positive faeces after sucrose flotation and individually confirmed through specific PCR and sequencing. The spatial distribution of E. multilocularis was studied using Kulldorff statistics. Echinococcus multilocularis eggs were identified mostly in fox faeces positive for E. multilocularis DNA by qPCR (n = 27/70) and only from 1 of 15 copro-samples from dogs and 1 of 5 from cats. The faecal prevalence of E. multilocularis DNA and eggs was overdispersed, with the same geographical patterns. These data suggest that E. multilocularis DNA and/or egg detection in carnivore faeces, mainly that of foxes, is appropriate in ecological studies of E. multilocularis transmission.