The first 1000 days (conception to 24 months) is when gut microbiota composition and eating patterns are established, and a critical period influencing lifelong health. The aim of this study is to examine the associations between food intakes and microbiota composition at the end of this period. Diet was quantified for 37 well-nourished Australian children aged between 2 to 3 years by using a food frequency questionnaire and 24 hr recalls. Both dairy and plant-based (fruit, vegetables, soy, pulses and nuts) food intakes were associated with distinct microbiota profiles. Dairy intake was positively associated with the Firmicutes:Bacteroidetes ratio, and in particular Erysipelatoclostridium spp., but negatively associated with species richness and diversity. Vegetable intake was positively associated with the relative abundance of the Lachnospira genus, while soy, pulse and nut intake was positively associated with the relative abundance of bacteria related to Bacteroides xylanisolvens. Fruit intake, especially apples and pears, were negatively associated with the relative abundance of bacteria related to Ruminococcus gnavus. In this cohort of young children dairy and plant based food intakes were found to be associated with altered microbiota composition. Further exploration is needed to elucidate the effect of these dietary and microbial differences on host phenotype.