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Matricaria aurea(Loefl.) Schultz Bip. (Asteraceae), known as golden chamomile, has been traditionally used for the treatment of various diseases. In this study, total phenolic, flavonoid, and tannin contents of total extract and different fractions of this plant were determined. The antioxidant, cytotoxic, and antimicrobial activities were also evaluated. Moreover, the phenolic profiles of selected fractions were determined by HPLC and LC-MS/MS analysis. Results demonstrated total phenolic contents of 37.8–57.2 mg GAE/g and total flavonoid contents of 3.0–111.2 mg QE/g. The ethyl acetate and methanol fractions (EF and MF) had the highest concentrations of phenolic, tannin, and flavonoid compounds. In both DPPH radical scavenging assay and phosphomolybdenum reduction assay, EF showed the best antioxidant activity, followed by MF. EF and MF indicated also the best antibacterial activities against Bacillus subtilis(MIC 1.56 and 12.5 mg ml−1) and Staphylococcus aureus(MIC 0.78 and 12.5 mg ml−1). Hexane fraction (HF) had no antibacterial effect. None of the samples had antifungal effect. MTT (3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay revealed for EF and HF the highest antiproliferative activities (IC50values ranged from 111.8 to 294.6 μg ml−1). The presence of chlorogenic acid, ferulic acid, and luteolin-7-O-glucoside in MF, and p-coumaric acid in EF was confirmed and quantified.