Colonization with multidrug-resistant organisms (MDROs) belonging to the genus Staphylococcus and the order Enterobacterales poses a particular threat to populations at risk. While previous studies focused on MDRO carriage among livestock or companion animals, respective epidemiological data on the general equine population are limited. Here, carriage of methicillin-resistant Staphylococcus aureus (MRSA) and extended spectrum beta-lactamase (ESBL) producing Enterobacteriaceae (ESBL-E) in non-hospitalized horses living on private farms in the rural area in Northwest Germany was assessed. Intranasal and perianal swab samples were cultured on solid chromogenic media directly and after enrichment in tryptic soy broth, respectively. S. aureus isolates were spa-typed, MRSA and ESBL-E were further classified by phenotypic and molecular methods. Additionally, a subgroup of the first 20 samples was used to isolate and characterize staphylococci other than S. aureus. Among 223 horses, fifteen (6.8%) carried S. aureus. Two isolates were identified as MRSA (0.9% of all horses, mecA-positive) and classified as spa types t011 and t6867, both known as members of the livestock-associated MRSA MLST clonal complex 398. Nine horses (4.0%) were colonized by ESBL-Escherichia coli positive for blaCTX-M and/or blaTEM. ESBL-E carriage was associated with prior antibiotic treatment (4/31 vs. 5/183; p = 0.0362) and veterinary examinations (4/31 vs. 5/183; p = 0.0362). In the subgroup, nine different staphylococcal species other than S. aureus were found. The high prevalence of ESBL-E. coli in non-hospitalized horses underlines the necessity to raise awareness for strain dissemination across different hosts in order to do justice to the “One Health” concept.