Impaired metabolism is the cause of several health issues, such as obesity, diabetes, dyslipemia, polycistic ovary syndrome, hypertension and other cardiovascular complications, creating a growing concern worldwide and leading to diminished life expectancy. New strategies are needed to increase the efficacy of prevention and management of these diseases. Personalized nutrition aims to prevent and manage chronic diseases by tailoring dietary recommendations taking into account the interaction between an individual’s biology, lifestyle, behavior, and environment. The progress in genomics, metabolomics, and gut microbiome technologies has opened opportunities in the use of precision nutrition to prevent and manage metabolic diseases. This review describes the perspectives of nutrigenetics, deep phenotyping, microbiota profiling, family and personal clinical cues, and a wide spectrum of data concerning metabolic personalization through omics technologies (metabolomics, epigenomics, metagenomics, and others) in tailoring dietary and lifestyle advices as a part of the prevention and management programs targeting metabolic diseases. The review also discusses advances and challenges in analyzing and monitoring eating habits, eating behavior, physical activity, and deep phenotyping, as well as the examples of successful applications of computer programs to implement mobile applications with personalized nutrition techniques in clinical practice.