Manuka honey from New Zealand is known for its exceptional antibacterial activity, which is due to high amounts of the 1,2-dicarbonyl compound methylglyoxal (MGO). MGO in manuka honey is formed via non-enzymatic dehydration from dihydroxyacetone (DHA) during honey maturation. MGO and DHA are highly reactive substances, leading to a variety of unique chemical reactions. During Strecker reaction between proline and MGO, 2-acetyl-1-pyrroline (2-AP), an important aroma compound, is formed. Using liquid-liquid extraction and gas chromatography-mass spectrometry analysis, 2-AP was identified unambiguously in manuka honey for the first time. Quantitation was carried out via external matrix calibration, using a synthetic 2-AP standard and artificial honey. The 2-AP concentration in 11 commercial samples of manuka honey ranged from 0.08 to 0.45 mg/kg. For manuka honey samples containing MGO in concentrations above 250 mg/kg, significantly higher amounts of 2-AP were found when compared to non-manuka honeys. When high amounts of MGO were artificially added to non-manuka multifloral honey, an increase of the 2-AP concentration from 0.07 to 0.40 mg/kg after 12 weeks of storage at 37 °C was observed, concomitant with a significant increase in the concentration of 5-hydroxymethylfurfural (HMF). No increase of 2-AP was found during storage at ambient temperature. 2-AP together with MGO can be a suitable parameter for the quality control of manuka honey.