In this review article, we provide an overview of the definition and application of fractional flow reserve (FFR), instantaneous wave-free ratio (iFR), coronary flow reserve (CFR), and index of microvascular resistance (IMR) in the diagnosis, prognosis, and management of coronary microvascular dysfunction. We discuss their respective limitations as it relates to microvascular dysfunction. In each section, we review the most recent evidence supporting their use in microvascular and epicardial coronary artery disease. We also highlight specific clinical conditions with emerging indications for the use of these indices, including in the setting of microvascular dysfunction due to acute myocardial infarction, heart failure with preserved ejection fraction, and post-cardiac transplant.