Ciliates tend to form stable associations with prokaryotes at the cellular level of organization. The ciliate Paramecium multimicronucleatum harbors the motile intranuclear endosymbiont Ca. Trichorickettsia mobilis (Rickettsiaceae) resistant to antibiotics. We assessed the effect of antimicrobial peptide complex FLIP7 produced by the larvae of the blue blow fly Calliphora vicina on the ciliate host viability and ability to maintain the endosymbiont. FLIP7 demonstrated a certain anti-ciliate activity, however, its administration failed to clear the endosymbionts from the host cells, surviving ciliates always keeping Trichorickettsia. Trichorickettsia-carrying ciliates appeared to be more resistant to FLIP7 and its chromatographic fractions, than Trichorickettsia-free strains, suggesting that Trichorickettsia might increase the host fitness. Alongside with the ovoid forms persisting in the host nucleus, another population of bacteria enriched in lipids was observed inside the cytoplasmic vacuoles. These forms were also registered outside the host cell, suggesting a possibility of horizontal transmission under stress. The data obtained support the belief that the symbiotic system between P. multimicronucleatum and Ca. Trichorickettsia mobilis is a perfect holobiont model to be used in further cytological and genetic studies.