The goal of this study is to synthesize, determine the structure, and examine the antimicrobial properties of novel Cu(II) and Au(III) complexes of 2,4-dithiouracil and its derivatives. These complexes were obtained by mixing aqueous solutions of the corresponding metal salts with the ligand dissolved in DMSO and aqueous NaOH, using a metal-to-ligand ratio of 1:4:2. The structures of the new compounds were analyzed by melting point determination, microwave plasma atomic emission spectrometry (MP-AES) for Cu and Au, inductively coupled plasma optical emission spectrometry (ICP-OES) for S, attenuated total reflection (ATR), solution and solid-state NMR, and Raman spectroscopy. The data for 2,4-dithiouracil obtained from the 1H NMR, 13C NMR, distortionless enhancement by polarization transfer spectrum (DEPT-135), proton–proton homonuclear correlation spectrum (1H-1H COSY), long-range 1H-13C heteronuclear multiple bond correlation experiment (HMBC), and heteronuclear single quantum coherence spectra (HSQC) aided the interpretation of the NMR data for the gold and copper complexes. Furthermore, the antimicrobial effect of the free ligands and their complexes was assessed against Gram-positive and Gram-negative bacteria, as well as yeasts.