Abstract Building energy simulation programs – in most cases – solve heat conduction through walls by considering one-dimensional heat flows, neglecting thermal bridges. The paper shows a new method for implementing bi-dimensional and three-dimensional heat transfer in dynamic energy simulation software, allowing a great improvement of their capabilities. The new procedure starts from the theory of state space representation of transfer functions, and then introduces simplifications for reducing computational time and the required CPU sources. Starting from a first case study, aimed to verify the achievable correspondence of the simplified new method compared to the original one, two common thermal bridges have been deeply analysed, comparing the proposed methodologies and numerical solution based on using finite volume methods. The investigated building structures determine bi-dimensional heat flows because of discontinuities in both materials and geometry. By comparing the achieved outcomes to those derived by much more onerous CFD studies, several cases changing grid refinement, timestep, ambient condition and so on, the proposed method shows its suitability, with maximum errors never higher than 4.5%, also under hourly-variable outdoor temperature and solar radiation.