Mycoplasma haemofelis is the most pathogenic feline hemoplasma species and a causative agent of infectious hemolytic anemia in cats. Current treatment protocols are effective in reducing M. haemofelis blood loads and clinical signs but consistent bacteremia clearance is rarely achieved. The aim of this study was to develop an antibiotic treatment protocol capable of clearing M. haemofelis bacteremia. Doxycycline and marbofloxacin treatment protocols were evaluated in chronically M. haemofelis infected cats in two pre-experiments and a controlled treatment study (main experiment) using five treated and four untreated cats. The blood bacterial loads in the main experiment were monitored weekly by real-time PCR for 203 days. Cats were treated with doxycycline (5 mg/kg bid orally) for 28 days. Cats that remained M. haemofelis PCR-positive or became positive again (all 5 cats in the main experiment) were switched to marbofloxacin treatment (2 mg/kg sid orally) for 14 days; then, all cats were PCR-negative. Immunosuppression after the antibiotic treatment did not lead to reactivation of bacteremia. Fine needle aspirates of different organs and bone marrow collected before and after immunosuppression were PCR-negative. Overall, 5 cats cleared bacteremia with doxycycline alone (showing lower bacterial loads at the treatment start), while 10 cats needed to be switched to marbofloxacin. Based on our results, we recommend doxycycline treatment (10 mg/kg up to 28 days) for clearance of M. haemofelis infection and monitoring bacterial loads by real-time PCR. Only if bacteremia persists or reoccurs, antibiotic treatment should be switched to marbofloxacin (2 mg/kg sid for 14 days).