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(1) Background: The objectives of this study were to evaluate the effect of several sessions of the antibacterial protocol of complex electromagnetic fields (CMFs) on planktonic <i>Candida albicans</i> and fungal ability, after treatment with CMFs, to adhere and proliferate on acrylic resin materials. (2) Methods: Planktonic overnight cultures of <i>Candida albicans</i> were subjected to different entities of CMFs treatments. Four test groups were compared: “p1”: treated only with the first program of the antibacterial protocol; “p1–p5” subjected to the first five programs; “1 antibacterial” received one complete session of the protocol and “2 antibacterial” received two complete sessions. After the treatments, the number of colony forming units (CFUs) were recorded. Then, <i>C. albicans</i> broth cultures were cultivated on polyacrylic resin discs and evaluated for CFUs and subjected to scanning electron microscope (SEM) analysis. (3) Results: Microbiological analysis showed that CMFs promoted a significant reduction of <i>C. albicans</i> CFUs when the protocol “p1–p5” was applied. No statistically significant differences between test groups were observed if the time of exposure to CMFs was increased. SEM observations and CFUs showed that CMFs treatments have the ability to reduce <i>C. albicans</i> adherence and proliferation on discs. (4) Conclusions: The CMFs showed an antifungal effect as well as a decrease in <i>C. albicans</i> adhesion on polyacrylic resin.