Plasma polypyrrole doped with iodine (PPy/I) and heparin (Hp) has been used as drugs in different ways in the human body. In this work, Hp was inserted into porous PPy/I to prepare biocompatible mixtures to potentially release Hp into the human body. The study was focused on the absorption and chemical interaction of Hp with PPy/I to find whether their structures suffer modifications in the carrying process. The absorption was performed by cryo-lyophilization immersing Hp in water with a 10:1 polymer/drug mass ratio. Once in contact, Hp went into the pores and partially coated the PPy/I surface. IR analyses of the mixtures on the surface showed that the functional Hp groups predominated over the polymer. The chemical interaction of both components was studied by XPS analyzing the energetic distribution of their atomic 1s or 2p orbitals. The results indicated that Hp interacted chemically with PPy/I losing the highest oxidized C1s, N1s and S2p chemical states in both components, forming new reduced ones with less multiple bonds or with more hydrogenated groups. S2p states were especially modified losing the most reactive states with 6 valences to form new more stable states with 2 valences. O1s orbitals behaved differently losing the most reduced chemical states forming new oxidized ones. These modifications suggest that the chemical reactivity of this PPy/I-Hp binary system was altered reducing the therapeutic capability of both components. This kind of studies should be done in all carrier-drug combinations to evaluate the possible chemical interaction between them.