Abstract Fossil fuels are unable to meet the current energy demands and polluting the environment with the emission of harmful gases. Therefore, clean energy technology is need of the modern era. One of the energy conversion devices is fuel cell which utilized fuel from renewable sources and convert into electricity in an efficient and clean way. However, for commercialization of this technology high operating temperature, degradation of electrodes and manufacture cost is the key challenges in conventional three layer fuel cell. Significant improvements have been made to reduce the cost and operating temperature by selecting suitable materials. Therefore, single layer fuel cell (SLFC) has been got much attention due to simple geometry. The mechanism inside the SLFC is still mystery which has been explained in this paper using quantum mechanical parameters like band gap and effect of particle size on charge transportation. In this research work, nanocomposite materials for single layer fuel cell have been synthesized by chemical routes. The x-ray diffraction shows the cubic perovskite structure with average crystallite size in the range of 23–37 nm. The particle size and surface area is found to be 23 nm and 86.42 m2 g−1, respectively. Raman spectrum of LBSCF-SDC shows a red shift compared to LBSCF and band gap of the composition 3LBSCF-7SDC is found to be 2.51 eV. Moreover, the conductivity of the sample 3LBSCF-7SDC has been found to be 0.02 Scm−1 at 750 °C. The quantum mechanical effects governing the working of single layer fuel cells are observed by different analyses. Photon confinement and Fano-Interactions phenomena resulted in a red shift using Raman analysis technique. The red shift in Raman spectrum is referred to a photon confined in a single layer fuel cell system. These effects are studied in single layer fuel cell for the first time with no previous analyses done in this newly field.