There is an increasing interest in the role of intestinal microbiome in human diseases and therapeutic agents' bioavailability, activity and toxicity. Epidemiological data show that the bioavailability of digoxin, a widely used agent for heart disease, varies among individuals. The inactivation of digoxin was found when it was incubated with gut bacterium Eggerthella lenta in vitro decades ago. However, the underlying mechanisms of digoxin inactivation are still unclear. A recent study using animal models uncovered this mystery, which suggested that arginine supplements might be a potential intervention in increasing digoxin activity by inhibiting the expression of cardiac glycoside reductase gene operons that inactivated digoxin. This perspective summarizes the connections among the intestinal microbiome, the digoxin inactivation, the metabolism of arginine. We also discuss several issues yet to be addressed in the future, making better strategies in the application of dietary arginine supplements for digoxin users.