Poly-NIPAm microgel particles with two different cross-linking densities were prepared with the classical batch polymerization process. These particles were adsorbed onto modified silica surfaces, and their nanomechanical properties were measured by means of atomic force microscopy. It was found that these particles have a hard core–soft shell structure both below and above the volume transition temperature. The core–shell-like structure appears due to a higher reaction rate of the cross-linker compared to that of the monomer, leading to depletion of cross-linker in the shell region. The microgel beads with lower average cross-linking density were found to be less stiff below the volume transition temperature than the microgel with higher cross-linking density. Increasing the temperature further to just above the volume transition temperature led to lower stiffness of the more highly cross-linked microgel compared to its less cross-linked counterpart. This effect is explained with the more gradual deswelling with temperature for the more cross-linked microgel particles. This phenomenon was confirmed by dynamic light scattering measurements in the bulk phase, which showed that the larger cross-linking density microgel showed a more gradual collapse in aqueous solution as the temperature was increased.