The increasing demand for bee-derived products such as honey and bee pollen has led to a rise in adulteration and mislabeling, making it essential to develop reliable tools for authentication. Lipids, which are found in both matrices, are potential biomarkers for tracing their origin and may be used for detecting fraud. In this work, a solid–liquid extraction using hexane:isopropanol (10:1, v/v) followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was optimized. The method was applied for tentative lipid screening of 15 honeys and 13 bee pollens showing a total number of lipids above 700, including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. For the first time, a principal component analysis was carried out for botanical and geographical origin, classifying most of the samples correctly. Additionally, the method was categorized as green (environmentally friendly) and blue (practical).