An in-rubber study of the interaction of silica with proteins present in natural rubber show that the latter compete with the silane coupling agent during the silanisation reaction; the presence of proteins makes the silane less efficient for improving dispersion and filler–polymer coupling, and thus influences the final properties of the rubber negatively. Furthermore, the protein content influences the rheological properties as well as filler–filler and filler–polymer interactions. Stress strain properties also vary with protein content, as do dynamic properties. With high amounts of proteins present in natural rubber, the interactions between proteins and silica are able to disrupt the silica–silica network and improve silica dispersion. High amounts of proteins reduce the thermal sensitivity of the filler–polymer network formation. The effect of proteins is most pronounced when no silane is used, but they are not able to replace a coupling agent.