Table olives are one of the most widespread fermented foods in the Mediterranean area, presenting an exponential increase in global consumption in the latest years. As a fermented product, its microbiota consists of a complex ecosystem, the composition of which depends on a multitude of factors and affects the quality attributes of the final product. The swiftly developing and constantly evolving field of omics technologies is being applied to unravel the profile of the microbial ecosystem and enable a deeper understanding of the fermentation process. In particular, the use of amplicon metagenomics facilitates the thorough analysis of the microbiota involved as it encompasses both culturable and unculturable microorganisms. Volatilomics aims at the identification and quantification of the volatile metabolites formed during fermentation with a direct involvement in the safety and quality evaluation of the food product. The integration of metagenomic and volatilomic data, through the application of bioinformatics can enhance the understanding of the interplay between the microbial profile and volatilome, resulting in a more comprehensive view of the system. This review summarized the overall amplicon metagenomics and volatilomics analytical approaches, along with the currently available bioinformatics tools for the data analysis in the field of table olives. Emphasis is given to the integration of amplicon metagenomic and volatilomic data employed to characterize the diversity of microbial populations and reveal the relationships between them and the volatile compounds. The latter may provide an extensive view of the microbial community dynamics, which is key in table olive fermentation and the microbiota’s functional properties. The potentiality to evaluate their effect in shaping the quality and unique features of the final product is highlighted.