Both the Maillard reaction (MR) and thermal treatment influence the nutritional value of milk. In this paper, the capability of polyphenolic berry extract (PBE) to inhibit MR in an ultra-high temperature (UHT) treated milk was investigated. Total polyphenol content and antioxidant capacity of blueberry (BE) and raspberry extracts (RE) were also tested. A gas chromatography-mass spectrometry (GC–MS) method was developed to monitor the MR product N ε-(carboxymethyl)-L-lysine (CML) and L-lysine (LYS). PBE was added to milk at 0.05 and 0.1% w/v prior to UHT processing. Data revealed that formation of CML was significantly reduced (23.4 ± 5.1%) by addition of 0.1% w/v BE. The final concentrations of LYS measured following the addition of PBE prior to thermal treatment were statistically similar to the control milk which was not subjected to thermal processing. Additionally, the metabolic profile of milk samples was investigated by GC–MS and visualised using ‘FancyTiles’.