The application of chemometrics, a widely used science in food studies (and not only food studies) has begun to increase in importance with chemometrics being a very powerful tool in analyzing large numbers of results. In the case of honey, chemometrics is usually used for assessing honey authenticity and quality control, combined with well-established analytical methods. Research related to investigation of the quality changes in honey due to modifications after processing and storage is rare, with a visibly increasing tendency in the last decade (and concentrated on investigating novel methods to preserve the honey quality, such as ultrasound or high-pressure treatment). This review presents the evolution in the last few years in using chemometrics in analyzing honey quality during processing and storage. The advantages of using chemometrics in assessing honey quality during storage and processing are presented, together with the main characteristics of some well-known chemometric methods. Chemometrics prove to be a successful tool to differentiate honey samples based on changes of characteristics during storage and processing.