We constrain the amplitude of primordial non-Gaussianity in the cosmic microwave background data taking into account the presence of foreground residuals in the maps. We generalize the needlet bispectrum estimator marginalizing over the amplitudes of thermal dust, free–free and synchrotron templates. We apply our procedure to Wilkinson Microwave Anisotropy Probe 5-year data, finding fNL= 38 ± 47 (1σ), while the analysis without marginalization provides fNL= 35 ± 42. Splitting the marginalization over each foreground separately, we found that the estimates of fNL are positively cross-correlated of 17 and 12 per cent with the dust and synchrotron, respectively, while a negative cross-correlation of about −10 per cent is found for the free–free component.