The occurrence of diseases is usually accompanied by changes in protein levels and types. These differentially expressed proteins can be used as biomarkers for the diagnosis and treatment of diseases. In recent years, luminescent iridium(III) complexes have attracted much attention in the field of protein-based disease diagnosis due to their excellent optical properties. In particular, affinity-based luminescent iridium(III) complexes have the advantage of evaluating protein information with minimal interference on their biological activities. In this review, we summarize the current advances in affinity-based luminescent iridium(III) complexes for the detection of disease-related proteins. Moreover, the future perspective for affinity-based iridium(III) complexes is discussed.