New Zealand mānuka honey is derived mainly from Leptospermum scoparium nectar and is valuable through accumulation of antibacterial methyl glyoxal (MGO). Mānuka honey also has a strong polyphenolic profile. Some phenolics act as chemical markers aiding verification of botanical origin as Leptospermum scoparium. A total of eight key chemical markers (DHA, MGO, 3-PLA, 4-HPLA, 2’-MAP, 2-MBA, Leptosperin and LepteridineTM) are found at higher levels in mono-mānuka honey than in multi-mānuka honey, with little or none in other floral honeys. These key markers signify mānuka honey quality and purity (i.e., monoflorality of L. scoparium). The quality and purity of mānuka honeys depend on multiple factors, largely determined by botanical source, which define the value of the final honey product. Available nectar is, in turn, influenced by geographic district and season. Wild harvest honey is naturally a mixture from different nectars. Honey quality varies among apiaries, between beehives and even in a honey frame. Current industry practice lumps all frames of the same apiary together for extraction. Potentially, “good” quality frames of mānuka honey could be mixed with “bad” quality frames. This bulked process can limit the monetary value of mānuka honey. Quality assessment of honey while still in the frame before bulk extraction is of great of interest to the honey industry to preserve the value of mānuka honey at source and to ensure authenticity. The current study used rapid and non-destructive methods such as NIR and fluorescence combined with chemometrics, machine learning and deep learning to evaluate mānuka honey in the frame. The study focuses on assessment of mānuka honey quality in two ways: 1) direct measurement of levels of eight key chemical makers; 2) indirect measurement of potency (based on UMFTM score) and purity (verification of botanical origin as L. scoparium) that are built from key chemical markers. Honey samples (n ~ 1656) representing 200 L drums, ea