Neem (Azadirachta indica) leaves have been widely proposed as a traditional medicine and many bioactive compounds have been isolated and characterized. Taking into account the high variability of the constituents content, which is influenced by many factors such as the environment and the crop production technology, a proper and fast analytical method is important for monitoring the chemical composition of the product. Here, we report, for the first time, the NMR-based metabolic fingerprinting of Neem leaves extracts obtained using two different extraction techniques, namely microwave-assisted and conventional extractions. To optimize the recovery of a large range of metabolites, three extraction times (10, 30 and 60 minutes) and three solvents (methanol, chloroform and acetone) were used. The microwave-assisted extraction gave the highest recovery in the case of methanol and acetone, whereas conventional extraction was the best procedure for chloroform.