Volatile organic compounds (VOCs) are secondary metabolites emitted by all living carbon-based organisms. These VOCs are of great importance in the agricultural sector due to their use as biofungicides and biopesticides. In addition, they can also be used as indicators of microbial contamination. The latter has rarely been studied; however, such a role is very relevant because it allows the timely application of corrective treatments that avoid food waste, the development of toxins dangerous to humans, and the design of biosensors. Gas chromatography–mass spectrometry (GC-MS), electronic nose (e-nose), and proton transfer reaction mass spectrometry (PTR-MS) are some of the techniques used to detect VOCs in fruits and vegetables contaminated by microorganisms. Therefore, the objective of this work is to deepen our knowledge of VOCs emitted by microorganisms in terms of their use as an indicator of microbial contamination of fresh agricultural products, as well as the analytical techniques used for their detection.