Antimicrobial resistance (AMR) is becoming more common in both bacteria and pathogenic protozoa. Therefore, new solutions are being sought as alternatives to currently used agents. There are many new ideas and solutions, especially compounds of natural origin, including essential oils. In the present study, the antiprotozoal activity of a mixture of essential oils (eucalyptus, lavender, cedar and tea tree), organic acids (acetic acid, propionic acid and lactic acid) and metal ions (Cu, Zn, Mn) were tested. As a model, protozoans were selected: Euglena gracilis, Gregarina blattarum, Amoeba proteus, Paramecium caudatum, Pentatrichomonas hominis. The tested concentrations of mixtures were in the range of 0.001–1.5%. The analyses show unexpected, very strong protozoicidal activity of combinations, presenting the synergy of compounds via determination of LD50 and LD100 values. Obtained mixtures showed significantly higher activity against protozoans, compared to chloramphenicol and metronidazole. Most of the analyzed samples show high antiprotozoal activity at very low concentration, in the range of 0.001–0.009%. The most effective combinations for all analyzed protozoans were the cedar essential oil and tea tree essential oil with a mixture of acids and manganese or zinc ions. Innovative combinations of essential oils, organic acids and metal ions are characterized by very high antiprotozoal activity at low doses, which, after further investigation, can be applicable for control of protozoan pathogens.