The polyene antifungal amphotericin B (AmB) exerts a powerful and broad activity against a vast array of fungi and in general displays a remarkably low rate of antimicrobial resistance. Aspergillus terreus holds an exceptional position among the Aspergilli due to its intrinsic AmB resistance, in vivo and in vitro. Until now, the underlying mechanisms of polyene resistance were not well understood. This review will highlight the molecular basis of A. terreus and AmB resistance recently gained and will display novel data on the mode of action of AmB. A main focus is set on fundamental stress response pathways covering the heat shock proteins (Hsp) 90/Hsp70 axis, as well as reactive oxygen species detoxifying enzymes in response to AmB. The effect on main cellular functions such as fungal respiration will be addressed in detail and resistance mechanisms will be highlighted. Based on these novel findings we will discuss new molecular targets for alternative options in the treatment of invasive infections due to A. terreus.