In this study, the antimicrobial agents of mono(hydroxyethoxyethyl)phthalate (M(HEEP)2) with different metal of M = Zn, Mn, Pb, and Ca were synthesized from diethylene glycol (DEG), phthalic anhydride (PA), and divalent metal acetates including calcium acetate, zinc acetate, manganese acetate, and lead acetate, respectively. The waterborne urethane oil (WUO) dispersions synthesized from linseed oil, diisocyanates (hexamethylene diisocyanate (HDI) and isophorone diisocyanate (IPDI)), dimethylolpropionic acid at NCO/OH molars of 0.9, by acetone processing method were described as in our previous report. The M(HEEP)2 antimicrobial agents as well as the commercial nanosilver powder were added into WUO dispersions as the antimicrobial coatings. The effects of various antimicrobial agents and dosages (0.0, 0.2, 0.6, 0.8, 1.0, 2.0, and 4.0 phr) on antimicrobial activity of WUO films against gram-negative bacterium of Escherichia coli, gram-positive bacterium of Staphylococcus aureus, brown-rot fungus of Gloeophyllum trabeum, and white-rot fungus of Lenzites betulina were assessed. In addition, the film properties of the best antimicrobial WUO coatings were also examined. The results showed that the antimicrobial agents of mono(hydroxyethoxyethyl) phthalate M(HEEP)2 (M = Zn, Mn, Pb, and Ca) powders should certainly be synthesized by FTIR, 1H-NMR, 13C-NMR, and energy-dispersive X-ray spectroscopy (EDS) identifications and the yields of them were 43–55%. The results also revealed that the WUO film synthesizing with HDI films containing Zn(HEEP)2 of 2.0 phr and Pb(HEEP)2 of 0.4 phr had the best antibacterial activity for E. coli and S. aureus, respectively. The IPDI films containing Zn(HEEP)2 of 1.0 phr had the best antibacterial activity for both E. coli and S. aureus. For antifungal activity, the WUO film synthesizing with HDI films containing Pb(HEEP)2 of 0.8 phr and Zn(HEEP)2 of 2.0 phr as well as IPDI films containing Mn(HEEP)2 of 0.2 phr and Zn(HEEP)2 of 4.0 phr had the best performances against G. trabeum and L. betulina, respectively. Comparing with commercial nanoAg powder, the Zn(HEEP)2 and Pb(HEEP)2 had a superior antifungal efficiency for G. trabeum and L. betulina, while it had a slightly inferior efficiency in the antibacterial activity for E. coli and S. aureus. On the properties of WUO films, adding metal-containing antimicrobial agents could slightly enhance the thermal stability, but lowered the gloss of all films, however, the Tg value increased for HDI film and decreased for IPDI film. In addition to this, they had no significant difference in the film properties including hardness, impact resistance, bending resistance, adhesion, mass retention, and light-fastness between the WUO films with and without adding antimicrobial agents.