Macroalgae live in tight association with bacterial communities, which impact most aspects of their biology. Clean, ideally axenic, algal starting material is required to control and study these interactions. Antibiotics are routinely used to generate clean tissue; however, bacterial resistance to antibiotics is increasingly widespread and sometimes related to the emergence of potentially pathogenic, multi-resistant strains. In this study, we explore the suitability of two alternative treatments for use with algal cultures: essential oils (EOs; thyme, oregano, and eucalyptus) and povidone-iodine. The impact of these treatments on bacterial communities was assessed by bacterial cell counts, inhibition diameter experiments, and 16S-metabarcoding. Our data show that thyme and oregano essential oils (50% solution in DMSO, 15h incubation) efficiently reduced the bacterial load of algae without introducing compositional biases, but they did not eliminate all bacteria. Povidone-iodine (2% and 5% solution in artificial seawater, 10min incubation) both reduced and changed the alga-associated bacterial community, similar to the antibiotic treatment. The proposed EO- and povidone-iodine protocols are thus promising alternatives when only a reduction of bacterial abundance is necessary and where the phenomena of antibiotic resistance are likely to arise.