Numerous marine organisms, including macroalgae, produce bioactive compounds. As chemical extraction processes do not distinguish between compounds originating from the alga and its associated microflora, a key step immediately prior to isolation of molecules, is elimination of epibionts from the alga studied. In chemical, ecological and biotechnological contexts, a clear identification of the source organism when there are symbiotic interactions occurs is crucial. We aimed to improve understanding of specific secondary metabolite production by macroalgae through development of a methodology for removing microbial epibionts immediately prior to chemical extraction without damaging algal cell surfaces (to avoid extraction of endogenous macroalgal compounds at this stage). Various solutions were tested: non-polar solvents (dichloromethane and hexane), alcohols (methanol, ethanol and isopropanol), oxidants (sodium hypochlorite, hydrogen peroxide and iodine) and a natural product (tea tree oil) at various concentrations and contact times. Five macroalgal species were employed: Chondrus crispus, Fucus serratus, Palmaria palmata, Saccharina latissima and Ulva lactuca. Scanning electron microscopy was used to evaluate the surface integrity. The best epibiont removal rate without damaging tissue was obtained with mixtures of ethanol (40–50%) and sodium hypochlorite (1%). Interestingly, macroalgal moisture content influenced treatment efficacy.