Honeydew honey is produced by bees (Apis mellifera) foraging and collecting secretions produced by certain types of aphids on various parts of plants. In addition to exhibiting organoleptic characteristics that distinguish them from nectar honey, these honeys are known for their functional properties, such as strong antioxidant and anti-inflammatory activities. Despite their importance, they remain poorly characterized in comparison with flower honeys, as most studies on this subject are not only carried out on too few samples but also still focused on traditional chemical–physical parameters, such as specific rotation, major sugars, or melissopalynological information. Since mass spectrometry has consistently been a primary tool for the characterization and authentication of honeys, this review will focus on the application of these methods to the characterization of the minor fraction of honeydew honey. More specifically, this review will attempt to highlight what progress has been made so far in identifying markers of the authenticity of the botanical and/or geographical origin of honeydew honeys by mass spectrometry-based approaches. Furthermore, strategies devoted to the determination of contaminants and toxins in honeydew honeys will be addressed. Such analyses represent a valuable tool for establishing the level of food safety associated with these products. A critical analysis of the presented studies will identify their limitations and critical issues, thereby describing the current state of research on the topic.