Bee products are increasingly demanded and valued for their nutritional properties and health benefits, which are directly related to the bioactive compounds they contain. However, this rising demand has been accompanied by widespread adulteration and mislabeling, which lead to illegal competition among producers and compromise product quality. Thus, the authentication of botanical and geographical origin is becoming increasingly important when it comes to marketing. Reliable analytical tools are therefore essential to determine the composition of bee products in order not only to enhance their nutritional value and health benefits but to ensure their traceability and authenticity. While several classes of bioactive compounds, such as amino acids, betaines and glucosinolates, have been previously studied and proposed as potential markers of their authenticity, lipids remain relatively unexplored. We present the development and optimization of a rapid and practical methodology for lipid profiling of honey and bee pollen. Solid–liquid extraction was combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), enabling broad lipid coverage with minimal sample handling. Optimization of instrumental parameters and sample treatment led to reproducible lipid profiles in both matrices. The proposed method was applied to 15 honey and 13 bee pollen samples of diverse botanical and geographical origins collected across Spain. More than 700 lipids were tentatively identified across all samples, including the five main families: fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. Principal component analysis (PCA) revealed clear clustering of the samples, allowing their classification according to both botanical and geographical origin.