This study presents the first case of the joint DNA metabarcoding of prey items and microbiome community analysis in wild juvenile fish. Juvenile European plaice (Pleuronectes platessa) were caught at 11 locations in the southern North Sea and eastern English Channel. Stomach fullness varied ontogenetically in time and space. Food uptake seemed to be slightly limited for the smallest plaice individuals up to a size of 20 to 30 mm. Furthermore, strong homogeneity for microbiome and prey item composition prevailed. Little seasonal, annual and regional (on-offshore/depth) variation was observed in prey item composition. Brown shrimp Crangon crangon made up >70% of the reads in all stomachs, length classes, regions, seasons and years. Offshore samples differentiated with a distinct lack of β-Proteobacteria in the gut microbiome. Based on a visual similarity network analysis, there was no observable correlation between prey item and microbiome composition, indicating that the microbiome composition wasn't driven by diet, but might be determined by the benthic bacterial community. DNA metabarcoding yields clear insights in the prey and microbiome composition of plaice, even for seemingly empty stomachs, and should therefore be considered for future dietary and microbiome studies.