There is no doubt that the current knowledge in chemistry, biochemistry, biology, and mathematics have led to advances in our understanding about food and food systems. However, the so-called reductionist approach has dominated food research, hindering new developments and innovation in the field. In the last three decades, food science has moved into the digital and technological era, inducing several challenges resulting from the use of modern instrumental techniques, computing and algorithms incorporated to the exploration, mining, and description of data derived from this complexity. In this environment, food scientists need to be mindful of the issues (advantages and disadvantages) involved in the routine applications of chemometrics. The objective of this opinion paper is to give an overview of the key issues associated with the implementation of chemometrics in food research and development. Please note that specifics about the different methodologies and techniques are beyond the scope of this review.