Skin infections are common complications in both humans and animals. Because of the increased incidence of multi-drug resistant (MDR) skin infections, essential oils have been suggested as potential alternatives to the classic antimicrobials. The goal of this study was to evaluate the minimum inhibitory and bactericidal/fungicidal concentrations (MIC and MBC/MFC) of commercially available products containing essential oils, zinc gluconate, or 4% chlorhexidine. Microbroth dilution technique was performed on clinical isolates of MDR Staphylococcus pseudintermedius (MDR-SP; n = 10), Pseudomonas aeruginosa (PA; n = 10), and Malassezia pachydermatis (MP; n = 10). For MDR-SP, essential oil-containing products showed median MICs of 1:240 and 1:320. The chlorhexidine shampoo had a MIC of 1:128,000 (0.312µg/mL), whereas zinc gluconate products had median MICs of 1:320 and 1:160. Three essential oil-containing shampoos (MBC 1:40), the zinc gluconate (MBC 1:40), and the chlorhexidine (MBC 1:64,000 [0.625µg/mL]) reached an MBC. For PA, essential oil-containing products showed median MICs of 1:30 and 1:80. The zinc-gluconate products had a median MIC of 1:160, whereas the chlorhexidine shampoo had a median MIC of 1:4,000 (10µg/mL). Only the zinc-gluconate products (MBC 1:80) and the chlorhexidine shampoo (MBC 1:2,000 [20µg/mL]) reached an MBC. For MP, essential oil-containing and zinc-gluconate products showed lower median MICs (1:4,800 and 7,200) for shampoos compared with other formulations (1:160 and 1:320), whereas the chlorhexidine shampoo had a median MIC of 1:80,000 (0.5µg/mL). These results suggest that natural topical compounds can be an effective alternative to treat skin infections in companion animals. Further in vivo studies are needed to clinically confirm this study's results.