Given the large amount of energy required in the building sector, an interesting opportunity to reach future sustainable energy systems is the path towards low energy buildings. This work proposes an approach for optimally integrating building-scale energy technologies (both traditional and renewable) to enhance the transformation of the existing buildings (often energetically inefficient) in low-carbon systems. The approach promotes a transition sustainable from both the economic and environmental perspectives. Both operation and design optimization are considered with the aim of suggesting the best set of capacity of the technologies to be installed taking into account the expected operations. The building-scale technologies are integrated with proper storage units: Li-ion batteries and thermal storage (latent heat, that requires low installation space). As a dispatchable renewable technology, a biogas small-scale combined heat and power unit is included in the system. Once the key role played by this component in meeting the loads is proved, an analysis of the impact of the cost of the primary energy carrier of this technology on the system design is carried out. Two optimization approaches have been adopted (both based on non-linear programming). Results show that operation costs can be reduced by up to 29%. The adoption of a combined approach that takes into account both operation and design optimization lead to a reduction in installation and operating costs by up to 27%. In the analyzed cases, the use of the combined optimization confirms that latent heat storage is more suitable to be installed than electric storage (about −4.5% cost).