Animal slaughtering is the most vital step in the preparation of chicken meat. The step ensures the meat is safe for human consumption since the procedure of animal slaughtering can affect the meat quality. In this study, we compare the quality of chicken meats obtained via two common slaughtering procedures: neck slaughtering (NS) and neck pocking (NP). The meat quality was assessed based on physicochemical analyses (ultimate pH, colour, heme iron content, drip and thaw loss measurements and TBARS value) and metabolite profiling (FTIR, GC–MS and UHPLC with PCA and PLS-DA). The study found that, relative to the NP-, the NS-chicken meat had slightly acidic pH, and much lower values of the following parameters: L* (lightness) (P = 0.023), heme iron content (P < 0) and TBARS (P < 0.01). Comparing FTIR spectra, the metabolite fingerprints of both meats looked slightly different. This was confirmed to be due to a set of differential metabolites present in the NS and the NP-chicken meats, as recorded by GC–MS and UHPLC-TOF-MS data after analyzing with PCA and PLS-DA. Compared to the NP, the NS-chicken meat was rich in metabolites with health benefits, including n-3-polyunstaurated fatty acids (PUFA), triglyceride (TG), cytadine and uridine. In addition, the NS-chicken meat also contained much lower concentrations of free amino acids. This is desirable as free amino acid-deficiency is able to suppress the production of biogenic compounds, a group of chemicals that produce toxicological effects on human heath when taken excessively.