This study describes a robust chromatographic authentication methodology for herbaceous pollen, employing gas chromatography–mass spectrometry (GC–MS), high‐performance liquid chromatography (HPLC) and high‐performance thin liquid chromatography (HPTLC) protocols. The comprehensive profiling of organic compounds not only distinguishes between different botanical sources but also establishes a reliable framework for quality control and assessment of herbaceous pollen authenticity. Traces of quercetin were detectable using HPTLC in Chaenomeles japonica, and the composition of the mobile phase led to distinct phenolic acid tracks in the extracts of free phenolic compounds. In Lonicera nummulariifolia, prominent chlorogenic acid signal and traces of 3,4‐dihydroxybenzoic acid were identified, along with the presence of vanillic, trans‐ferulic, p‐coumaric and p‐hydroxybenzoic and sinapic as phenolic acid standards. The HPLC chromatogram identified six peaks representing bioactive phenolic compounds such as gallic acid measuring 5.89 ± 0.56 mg g−1, hydroxybenzoic acid 2.39 ± 0.78 mg g−1 and caffeic acid 2.83 ± 0.11 mg g−1. The combined use of GC–MS, HPTLC and HPLC techniques provides a powerful and reliable means of authenticating the botanical origin of herbaceous pollen, offering valuable insights for quality control and ensuring the accuracy of botanical source identification.