Atomic force microscopy (AFM) was employed to probe the interaction between recombinant ferritin molecules immobilized on an AFM tip and surface-modified silicon substrates. Force-distance curve profiles demonstrated for the first time the controllability of long-ranged ferritin-substrate interactions and the amount of ferritin molecules adsorbed on a substrate by modifying the amino acid sequence in the N-terminal domains. In addition, we proposed that the decoration of substrate surface with self-assembled monolayers (SAMs) also helped in controlling the ferritin-substrate interaction and the resulting adsorption amount. Our important finding is that the amount of ferritin adsorbed cannot be predicted simply from the zeta potentials of a ferritin molecule and substrate, and that the flexibility of the surface polar groups on a Si substrate is an important factor that governs the amount of the adsorption. Based on the analysis of force-distance profiles, we discuss what kind of force dominates the long-ranged and short-ranged interactions between ferritin and silicon substrates. These provide insights and lead to a deeper understanding of the factors to govern the adsorption of ferritins onto solid substrates.