Sodium percarbonate (SP) is a relatively low-cost and stable solid oxidizer with a small environmental burden. It is often included in cleansers for sanitizing circulating water pipes and as bleaching reagents in laundry, although the bactericidal effect of SP is lower than that of chlorine-based agents. 2-[Bis(carboxymethyl)amino] propanoic acid-chelated copper (MGDA-Cu) was added to increase the effect of SP. The addition of 12 µM MGDA-Cu increased the bactericidal effect of 0.5 wt% SP against Staphylococcus aureus even in the presence of 0.3 wt% BSA, which is an experimental model of organic stain to protect bacteria from SP. MGDA-Cu was effective against Escherichia coli only in the absence of BSA and showed little effect against Bacillus subtilis. It enhanced the effect of SP to decrease the viscosity of sodium alginate, which is one of the major components of biofilms. The effect of MGDA-Cu on sanitization was also evaluated by 16S rRNA amplicon sequencing of the bacterial flora of the biofilm on an experimental model of a circulating water pipe. The structure of the bacterial flora was more influenced by a cleanser containing both MGDA-Cu and SP than a cleanser with only SP, suggesting that MGDA-Cu increases the sanitization effect.