Recent investigation approaches, based on High-Throughput Sequencing (HTS) technologies, allow to develop in-depth analysis of food microbiota/microbiome. HTS, which identify the modern Next Generation Sequencing (NGS) techniques, contribute to food investigation advances by allowing to produce a larger volume of data at a price that is decreasing. This contribute offers an overview about the latest and most innovative techniques for analyzing food microbiota. Furthermore, the impact on food microbiology of omics approaches based on HTS is discussed. Relevant metagenomics, metatranscriptomics, metaproteomics studies concerning different food application fields are treated. The current scenario and pregnant omics and multi-omics works are highlighted, showing the usefulness to adopt an integrated multi-omics approach in different food microbiology areas, especially in food quality and safety. In this context, nowadays, food is more and more considered not only as a source of energy but also as an affordable way to prevent diseases. Finally, some technical limitations of multi-omics methods are outlined. If in the past an integrative omics approach was not feasible because of the lack of expertise and technical limitations, the current technological advances offer high performances in terms of standardization to investigate a wide data set coming different platforms.