Intertidal mussels form complex relationships with microorganisms that influence host health and ecosystem functions like nutrient cycling. Endolithic cyanobacteria are microbes that colonize and bore into mussel shells with divergent effects on mussel health. They normally act as parasites, eroding and damaging mussel shells, but the relationship with the mussel host becomes mutualistic under thermal stress because shell erosion indirectly protects mussels from warming. It is not known how the activity of endolithic cyanobacteria affects the overall composition of the mussel shell microbiome. We hypothesized that biological filtering by living mussel hosts can limit cyanobacterial erosion and buffer the overall microbiome against abiotic variation throughout the intertidal zone. We tested if the mussel shell microbiome and interactions with parasitic endoliths differ between live and killed mussel hosts across geographic locations and at different elevations within the intertidal zone using transplant experiments and 16S rRNA amplicon sequencing. We show that shell erosion but not microbiome composition or abundance of endolithic cyanobacteria is modulated by living mussels. Instead, we find geographic location and intertidal elevation influence the composition of the mussel shell microbiome more strongly than biotic interactions. Our findings indicate that abiotic factors, particularly temperature, are a dominant selective filter for microbial community interactions with the external surface of an important marine foundation species.