: Chenopodium murale is a medicinal herb with biological functions that has been studied with common extraction methods. However, studies on Iraqi C. murale (ICM) have not yet been reported. Microwave-assisted extraction (MAE) was used as a green extraction method for the first time with C. murale. The phytochemical components were profiled by GC-MS, which showed about 11 compounds. The highest peak occurred for compound 6 (phytol, acetate), followed by compounds 9 and 10, which belong to the same compound (hepatocosane). The ethanol extract displayed antioxidant action with IC50 = 102.3 µg/ml, which was compared to vitamin C as a positive control (IC50= 79.69 µg/ml). We tested the toxicity of ICM against two types of cancer cell lines, breast cancer (MCF-7) and liver cancer (HACM), for which the IC50 values were estimated as 1504 and 1267 µg/ml, respectively. Late apoptosis values were 73.4 and 58.5 for MCF-7 and HCAM, respectively, and cell cycle arrest occurred in the G1 phase for HCAM and the G2 phase for MCF-7. The results were compared with control cells. In vitro, normal kidney cells showed limited toxicity from the extract, which was compared with highly toxic doxorubicin as a positive control. The results suggest that the MAE method for ICM produced selective bioactive compounds, which may behave as potential natural anti-breast and anti-liver cancer agents. The results could help in the development of future investigations with regular doses to prevent liver and breast cancer.