Due to the wide variation in geographic and climatic conditions, the search for high-performance bituminous materials is becoming more and more urgent to increase the useful life of pavements and reduce the enormous cost of road maintenance. Extensive research has been done by testing various bitumen modifiers, although most of them are petroleum-derived additives, such as polymers, rubbers and plastic, which in turn do not prevent oxidative aging of the binder. Thus, as an alternative to the most common polymeric rheological modifiers, selected binder additives falling in the categories of organosilane (P2KA), polyphosphoric acid (PPA) and food grade phospholipids (LCS) were homogeneously mixed to a base bitumen. The goal was to analyse the micro-morphology of the bitumens (neat and modified) subjected to different cooling rates and to find the corresponding correlations in the mechanical response domain. Therefore, microstructural investigations carried out by Atomic Force Microscopy (AFM) and fundamental rheological tests based on oscillatory dynamic rheology, were used to evaluate the effect of additives on the bitumen structure and compared with pristine binder as a reference. The tested bitumen additives have been shown to elicit different mechanical behaviours by varying the cooling rate. By comparing rheological data, analysed in the framework of the "weak gel" model, and AFM images, it was found that both P2KA and PPA altered the material structure in a different manner whereas LCS revealed superior performances, acting as "mechanical buffer" in the whole explored range of cooling rates.