(1) Background: Slightly acidic electrolyzed water (SAEW) is an effective and safe sterilizing solution. Its active component is hypochlorous acid (HOCl) which has been proved to exhibit a strong disinfectant activity. In this research we evaluated the effectiveness of SAEW in the removal of Methylobacterium mesophilicum, Rhodotorula mucilaginosa and Cladosporium cladosporioides, responsible for pink-colored biofilm and black mold in households. (2) Methods: Two concentrations of SAEW, 20 mg/L and 40 mg/L, were tested against M. mesophilicum, R. mucilaginosa and C. cladosporioides. In vitro experiments and mesh experiments were conducted to test the effectiveness of SAEW. (3) Results: The test results showed that 40 mg/L SAEW was effective in removing R. mucilaginosa and C. cladosporioides, with the population decreasing by approximately two orders of magnitude. For M. mesophilicum, resistance towards SAEW was observed; to obtain a 1.3 order of magnitude decrease in bacterial population, washing 5 times with 40 mg/L SAEW was necessary. Mesh experiments showed that SAEW can remove black mold; (4) Conclusions: Overall results indicated that SAEW was particularly effective for R. mucilaginosa and C. cladosporioides species commonly found in Japanese households.