Electrical energy storage is an attractive technology for complementing domestic scale Combined Heat and Power (CHP) because when CHP is dispatched to meet the heating load, the storage can reconcile any mismatch between the electrical load and CHP generation. Hybridization of electrical storage technologies reduces the compromise between power and energy density and extends storage system lifetime but necessitates a more complex control scheme. This paper proposes a novel control scheme for a domestic battery-supercapacitor hybrid energy storage system (HESS) for use with micro-combined heat and power (micro-CHP) generation. The proposed HESS controller utilizes the low frequency component of the supercapacitor voltage to generate the battery reference current, which not only allocates low frequency power to the battery but also simultaneously maintain the battery current and the supercapacitor voltage within their predefined limits. The negative effects of the 100 Hz ripple component in the supercapacitor current, such as overheating and increased converter losses have been hitherto neglected in the literature and are addressed here for the first time by adding a 100 Hz band-stop filter in the supercapacitor controller. Simulink simulations and signal hardware-in-the-loop (SHIL) real-time simulations have been conducted to demonstrate the effective operation of the HESS.