ABSTRACT The aims of this study were analysis of the secondary metabolite products of Achillea millefolia and Glycine max and evaluation of Anti-fungal activity. The FTIR analysis of Achillea millefolia proved the presence of functional group assignment Alkenes, Alkyl halides and Alkane with Intensity 779.24 Bending (Strong =C–H), 1018.41 Stretch (Strong C-F), 1074.35 Stretch (Strong C-F), 1153.43 Stretch (Strong C-F), 1313.52 Stretch (Strong C-F), 2927.94 Stretch (Strong C-H) The FTIR analysis of Glycine max proved the presence of functional group assignment Alkyl halides and Alkane with Intensity 1016.1 Stretch (Strong C-F), 1029.2 Stretch (Strong C-F), 1238.1 Stretch (Strong C-F), 1373.7 Stretch (Strong C-F), 2920.4 Stretch (Strong C-H). Zone of inhibition (mm) of test bacterial strains to Achillea millefolia bioactive compounds and standard antibiotics were (4.970±0.32), (3.115±0.13), (4.871±0.15), (4.766±0.31), and (3.990±0.22) uses Achillea millefolia bioactive compounds, and (1.001±0.09), (1.771±0.41), (1.008±0.12), (0.009±0.01), and (2.001±0.13) uses Rifambin, and (1.008±0.11), (2.682±0.29), (2.860±0.13), (1.037±0.21), and (1.000±0.10) uses Streptomycin, and (0.730±0.12), (1.000±0.46), (0.330±0.10), (2.000±0.11), and (0.084±0.10) uses Kanamycin, and (1.104±0.26), (1.996±0.27), (1.009±0.10), (1.005±0.15), and (1.007±0.11) uses Cefotoxime for Staphylococcus aureus, Escherichia coli, Proteus mirabilis, Klebsiella pneumonia, Pseudomonas eurogenosa respectively. Zone of inhibition (mm) of test bacterial strains to Glycine max bioactive compounds and standard antibiotics were (3.007±0.21), (4.006±0.14), (5.000±0.30), (3.089±0.21), and (4.000±0.23) uses Glycine max bioactive compounds, and (2.905±0.10), (2.9001±0.12), (2.006±0.12), (1.972±0.10), and (3.719±0.14) uses Rifambin, and (2.127±0.10), (1.000±0.11), (1.991±0.10), (2.994±0.11), and (0.988±0.10) uses Streptomycin, and (1.069±0.09), (2.961±0.10), (1.094±0.10), (3.190±0.11), and (1.009±0.10) uses Kanamycin and (2.000±0.11), (1.000±0.11), (2.371±0.11), (0.077±0.10), and (2.113±0.12) uses Cefotoxime for Staphylococcus aureus, Escherichia coli, Proteus mirabilis, Klebsiella pneumonia, Pseudomonas eurogenosa respectively.