The thermoresponsive behaviour of cross-linked poly(N-isopropylacrylamide) (pNIPAm) nanogels makes these materials particularly attractive for a variety of applications. Literature data report the use of different methodologies for preparing nanogels, which can be divided into heterogeneous and homogeneous polymerisation approaches. Heterogeneous polymerisation occurs above the volume phase transition temperature (VPTT) of pNIPAm due to water expulsion from the network of the forming polymer. On the contrary, homogeneous polymerisation is conducted below the VPTT, so that the nanogel is in the swollen state during the polymerisation process. Here, we study the effect of phase separation during polymerisation, which reveals a significant influence on the particle size and internal structure, as well as on the thermoresponsive and interfacial behaviour of pNIPAm nanomaterials. We propose that heterogeneous polymerisation leads to preferential localisation of hydrophilic initiator residues on the particle surface, while during homogeneous polymerisation, the initiator groups are distributed within the nanogel network. These results highlight the importance of the choice of polymerisation temperature as well as initiator for the synthesis of pNIPAm gels, as this significantly affects their characteristics and application.