Food integrity could be jeopardized by different types of food frauds. The concept of food integrity is composed of three pillars: (i) food quality, i.e., number of features, objective and subjective, of food that are acceptable to consumers and meet their expectations; (ii) food authenticity, namely the ability to follow the movement of a feed or food through specified stage(s) of production, processing, and distribution; and (iii) food safety, which is the probability of not becoming ill after consuming a food. Food fraud, i.e., modifications of food characteristics and/or ingredients, can affect the quality, authenticity and safety of food products. Moreover, these practices can affect consumers’ expectations and trust. In this review, applications of vibrational spectroscopy- (NIR and FT-IR) and proton transfer reaction mass spectrometry (PTR-MS) for food quality, authenticity and safety analysis will be discussed. Examples of how vibrational spectroscopy and proton transfer reaction – mass spectrometry applied to food integrity analysis will be given with regards to oils, milk and dairy products, and coffee.