The present study intends to investigate and analyze the main issues affecting a conjugategradient optimisation method (CGM) for parameter heat flux estimating applied to someexperimental tests carried out on single- and multi-injector combustion chambers at theInstitute of Propulsion of Flight (LFA) at the Technische Universität München (TUM).Each optimisation steps implemented in a Matlab code by Perakis et al. have been explainedin detail. Hence, the code has been modified with the purpose to make it fasterand more accurate and than it has been tested with a numerical function simulating heatflux rising along combustion chamber. An analysis of the nozzle boundary condition hasbeen performed to estimate errors that occurr by assuming it adiabatic.