Excessive sucrose consumption is associated with numerous health problems, including dental caries, and is considered to play a critical role in shaping the human microbiota. Here, we aimed to confirm the association between sucrose exposure and oral microbiota profile, develop a short food-based index capturing variation among sucrose consumers and validate it against oral microbiota and dental caries in a derivation cohort with 16- to 79-year-old participants (n = 427). Intake and food preferences were recorded by questionnaires and saliva microbiota by 16S rDNA sequencing. Taxonomic similarities clustered participants into five clusters, where one stood out with highest sucrose intake and predicted sugar related metabolic pathways but lowest species diversity in the microbiota. Multivariate modelling of food intake and preferences revealed foods suitable for a sucrose index. This, similarly to sucrose intake, was related to bacterial pattern and caries status. The validity of the sucrose index was replicated in the population-based Gene-Lifestyle Interactions in Dental Endpoints (GLIDE, n = 105,520 Swedish adults) cohort. This suggested that the index captured clinically relevant variation in sucrose intake and that FFQ derived information may be suitable for screening of sucrose intake in the clinic and epidemiological studies, although adjustments to local consumption habits are needed.