The increase in prevalence of staphylococcal antimicrobial resistance has been also associated with pyoderma in dogs, and prolonged antibiotic treatment, as often needed in severe cases of pyoderma, has been related to influencing possible development of multidrug resistance (MDR). Fluorescent light energy (FLE) has been indicated to improve pyoderma lesions as adjunct therapy to systemic antibiotics. In the present study, we evaluated the effect of FLE on clinical signs of MDR canine deep pyoderma (CDP) and interdigital furunculosis (CIF) when administered as solely management. Sixteen client-owned dogs affected by CIF (five dogs) and CDP (eleven dogs) were scored using a dedicated scoring system and received a single FLE applications twice weekly, until clinical resolution was achieved. Mean time to achieve complete resolution was 5.20 ± 3.56 weeks (median 3 weeks) for CIF cases and 4.18 ± 1.47 weeks (median 4 weeks) for CDP ones. FLE shows promise as an aid to managing clinical signs while reducing reliance on antibiotics for MDR CDP and CIF. In this study, FLE was responsible for the decrease in lesion scores and resolution of MDR pyoderma infection without any adjunct therapy, having a potential useful role to play in antibiotic stewardship programs, efficiently promoting complete clinical resolution of MDR lesions while optimizing the use of antibiotics.