Tarhana is a fermented cereal product in which other ingredients vary depending on the traditional regional formulation. We aimed to evaluate associated relationships between metabolites and microbiota of five different Tarhana recipes belonging to Isparta, Maraş, Bursa, Kastamonu, and Uşak regions by collecting 19 samples during their fermentation process. The microbiota was investigated using metagenomics by high-throughput sequencing at species level showing Pediococcus acidilactici in Bursa, Lactiplantibacillus plantarum in Kastamonu, and Levilactobacillus namurensis and Levilactobacillus zymae in Uşak Tarhana were dominant. Also, Kluyveromyces in Isparta and Maraş, Saccharomyces in Bursa, and Issatchenkia in Kastamonu Tarhana types had the highest relative abundances. Uşak type contained the highest amounts of lactic, succinic, and acetic acids, respectively, which were also the major organic acids of all samples. Integrative analysis of multiple omics datasets revealed that Tarhana samples differing in biodiversity could be significantly clustered according to Tarhana type and production difference.