The consequences of tip–substrate interactions are investigated using large‐scale molecular dynamics simulations for a large (001) gold tip and a Ni(001) surface. The simulations reveal processes of adhesive contact formation upon approach of the tip to the substrate, tip elongation, and formation of an extended ordered neck upon retraction of the tip from contact, (111) reconstruction of the interfacial gold layers and the atomistic mechanisms of tip flattening and increase in contact area upon compression past the adhesive contact point. The hysteresis in the force versus tip to sample distance relationship, found upon approach and subsequent separation of the tip from the sample, is related to processes induced by adhesion and intermetallic bonding. The atomic‐scale mechanisms underlying the jump‐to‐contact phenomenon at small tip to surface separation (∼4.2 Å) and of the inelastic processes and structural transformations involved in tip elongation, neck formation, and tip compression are discussed, and the results are compared to our earlier studies of a nickel tip interacting with a gold surface.