There is an ever-increasing trend in advanced food analysis and foodomics to use more and more sophisticated analytical platforms that generate large and complex data structures, which in turn require more and more sophisticated data analysis tools for converting data into information. The choice of multivariate chemometric methods is primarily determined by the design of the study, type of the data, and the conclusions sought. In order to validate multivariate models, scientists are required to have basic chemometric knowledge and to be familiar with the variance structure of the investigated data. This review outlines some of the key aspects of applying common chemometric methods used within foodomics and provides selected examples of current applications. The review aims to provide simple insight into various multivariate methods and to illustrate pros and cons of unsupervised and supervised methods. The main analytical platforms used in foodomics are briefly discussed from the application point of view and the utilization of the generated data is illustrated. In addition, advanced data pre-processing tools, prior to multivariate analysis, are explained and relevant tools are demonstrated.