Herein, we report the fabrication of nanometer-sized reduced graphene oxide (rGO) spots by swift heavy-ion (SHI) bombardment. Such structures can be considered graphene quantum dots (QDs) embedded in a non-conducting matrix. Both the number density and the diameter of the rGO spots can be tailored by a suitable choice of irradiation parameters (i.e., ion type, fluence, and energy). The degree of graphene oxide defunctionalization by SHIs with different energies scaled well with the deposited electronic energy density. The resistance of the samples decreased nonlinearly with increasing ion dose and, at fluences above 1013 ions/cm2, was orders of magnitude lower than the initial value. An increase in the electronic stopping power of the ion resulted (i) in suppression of the structural ordering at low fluences and (ii) in increased amorphization efficiency and formation of sp-hybridized carbon chains of both polyynes and polycumulenes at high fluences. A hypothesis suggesting that the sp-C chains are bridges joining opposite sides of nanoholes created inside the track core and thus assuming the formation of a coupled QD-antidot system is presented. These phenomena were found to be absent in comparative experiments with 200 keV Xe ion irradiation, i.e., in the nuclear stopping regime.