Functionalization of medical devices with biomolecules is a key strategy to control implant outcomes, for instance, polyphenols can produce fast osseointegration and reduce both the infection risk and inflammatory response. This paper is designed to evaluate the role of calcium ions and surface features in surface functionalization with a red pomace extract. An in-depth investigation of the binding mechanism between surfaces and polyphenols was also performed. A smooth Ti6Al4V alloy was used as a control substrate and compared with a bioactive and nanotextured chemical-treated Ti6Al4V alloy. Solutions with and without the addition of calcium ions were used for functionalization. The results showed that polyphenols were adsorbed in all cases, but in a larger amount in the presence of calcium ions. The functionalized surfaces were hydrophilic (contact angles in the range of 45–15°) and had isoelectric points at pH 2.8–3.1. The acidic hydroxyl groups on the chemically treated titanium alloy favored the chemisorption of complex compounds of flavonoids and condensed tannins with calcium ions, through a bridging mechanism, and made desorption sensitive to pH. On the smooth surface, the absence of reactive functional groups led to a lower amount of adsorbed molecules and a physisorption mechanism. Selective physisorption of phenolic acids was supposed to be predominant on the smooth surface in the presence of calcium ions in the solution.