Honeybee venom (HBV) is a product of natural origin with an extremely complex composition. It exhibits several beneficial pharmacological properties, for example anti-inflammatory, antimicrobial, antidiabetic, anti-arthritic, and anti-tumour activities. On the other hand, HBV contains highly allergenic components, including melittin, which makes up more than 50% of its dry weight. Despite many studies conducted, HBV's components and mechanism of action are not yet fully known and understood. Therefore, to enhance the safety of its therapeutical applications, it is essential to establish HBV's composition and biological properties. Many analytical techniques and methods have been reported as potentially useful for the determination of new HBV constituents. Studies focus mainly on the analyses of the HBV proteome and metabolome. Also, properties of its components when applied to the skin, as well as its allergenicity, are being studied. Currently, the most commonly used methods for HBV analysis include high-performance liquid chromatography and mass spectrometry. Choosing the correct and most applicable method for HBV analysis is of great importance in order to obtain in-depth results crucial for the understanding of its mechanism of biological action. The diversity of chemical compounds in HBV also entails an appropriate sample preparation at the pre-analytical stage. In order to summarise the latest knowledge on techniques for the analysis of complex natural products, on the example of HBV, this review paper discusses the modern analytical tools of HBV characterisation, focusing on metabolomic and proteomic studies, topical applications, investigation of venom allergies, and the prospects for future research.