Background Myrtle (Myrtus communis L) may constitute an interesting dietary source of health protective compounds. Microwave-assisted extraction (MAE) of total phenolic compounds (TPC) from myrtle leaf, stems, pericarp, and seeds was studied and the results were compared with those of the conventional method extraction (CME) in terms of extraction time. Methods Extraction yield/efficiency and antioxidant activity were measured using radical scavenging assay (DPPH•) and reducing power. Results The results show that the MAE was higher in terms of saving energy, extraction time (62 s) and extraction efficiency of bioactive compound compared to CME (2 h). Leaf presented the optimum content of total phenols (250 mg GAE.g-1 DW) and flavonoids (13.65 mg GAE.g-1 DW). However, the anthocyanin content was most important in pericarp extract (176.50±2.17 mg Cyd-3-glu g-1 DW). The antioxidant activity was important in all parts, mainly in leaves. The results indicated that appropriate microwave treatment could be an efficient process to phenolic compounds recovery and thus, better the antioxidant activity of myrtle extract. Conclusions Principal component analysis (PCA) applied to the experimental data shows that the distribution of the myrtle phenolic compounds depended on their plant part localization as well as the extraction method.