The commensal microbes inhabiting a host can interact with invading pathogens and host physiology in ways that alter pathogen growth and disease manifestation. A prior study in house finches (Haemorhous mexicanus) found that intact ocular microbiomes were protective against conjunctival infection and disease caused by Mycoplasma gallisepticum (MG). Here, we experimentally examined whether protective effects of the resident ocular microbiome vary with the dose of invading pathogen. We hypothesized that commensal protection would be strongest at low MG inoculation doses because the resident microbiome would be less overwhelmed by invading pathogen. Our five MG dose treatments were fully factorial with an antibiotics treatment to perturb and knock down resident microbes just prior to MG inoculation. Our pathology and pathogen load results were inconsistent with those from prior work that found protective effects of the ocular microbiome against MG inoculation. Unexpectedly, we found a trend toward lower pathology in birds with antibiotic-perturbed resident microbiomes, regardless of invading pathogen dose. Amplicon sequencing data indicated that birds began this study with resident ocular microbiomes distinct from those previously reported in our system. Here, the antibiotics may have knocked down resident ocular community members that facilitate rather than protect against MG, leading to a reduction and even a potential reversal in the microbiome’s protective capacity. The lack of repeatability of protective effects of the ocular microbiome in house finches reveals the sometimes-limited generalizability of ecological results and the likely context dependency in many symbiotic interactions.