The aim of the present study was to examine the efficiency of different decontamination-cleaning protocols on blood-soiled catheters used for interventional cardiology. Electrophysiology and cardiac ablation disposable devices were contaminated with bacteria-spiked human blood and underwent four different pre-sterilization protocols, including a chlorine-releasing agent, a polyphenolic emulsion, and an enzymatic detergent. Treated samples were examined by optical microscopy, scanning electron microscopy and transmission electron microscopy to identify and characterize biological and inorganic residuals. The use of chlorine as a first treatment caused denaturation of serum proteins and adherence of blood components to the surface of the device, thus hindering the cleaning efficiency of subsequent treatments with enzymatic detergents. An enzymatic/chlorine protocol was more efficient, but was considered to be a greater risk to healthcare staff. Polyphenolic-based treatments had the highest level of efficiency in bioburden removal, but interaction and adsorption of this class of chemicals onto biopolymers might lead to serious concerns about toxicity on subsequent reuse. Adequate pre-sterilization cleaning is fundamental for sterilization success and high-resolution electron microscopy can provide significant and detailed information about the efficiency of chemicals used for cleaning a blood-soiled device.