Chronic septic arthritis caused by methicillin-resistant Staphylococcus aureus (MRSA) is characterized by persistent infection, dysregulated host immunity and progressive joint destruction. However, the membrane-associated proteomic features that distinguish host cells harboring intracellular MRSA from neighboring cells exposed to the same infectious microenvironment remain incompletely understood. In this study, a murine model of chronic septic arthritis was established using GFP-expressing MRSA. Cells isolated from infected joint tissues were separated by fluorescence-activated cell sorting into GFP-negative and GFP-positive populations. The GFP-negative population represented cells from the infected joint microenvironment without detectable intracellular GFP signal, whereas the GFP-positive population represented cells containing detectable intracellular GFP-MRSA. Membrane-enriched protein fractions from both populations were isolated and subjected to liquid chromatography–tandem mass spectrometry for comparative membrane proteomic profiling. Differentially abundant membrane-associated proteins and biological pathways related to transmembrane transport, redox homeostasis, innate immune responses, phagosome–lysosome function, protein homeostasis and host–pathogen interactions were characterized. Particular attention was given to membrane transporters and immune-regulatory proteins associated with intracellular bacterial persistence. This dataset provides an in vivo membrane proteomic resource for identifying intracellular MRSA-associated remodeling of host-cell membrane protein networks during chronic septic arthritis.