Emission line spectra from HII regions are often used to study the metallicity of star-forming regions, as well as providing a constraint for temperatures and luminosities of the ionizing sources. Empirical metallicity diagnostics must often be calibrated with the aid of photoionization models. However, most studies so far have been carried out by assuming spherical or plane–parallel geometries, with major limitations on allowed gas and dust density distributions and with the spatial distribution of multiple, non-centrally located ionizing sources not being accounted for. We compare integrated emission line spectra from our models and quantify any systematic errors caused by the simplifying assumption of a single, central location for all ionizing sources. We find that the dependence of the metallicity indicators on the ionization parameter causes a clear bias, due to the fact that models with a fully distributed configuration of stars always display lower ionization parameters than their fully concentrated counterparts. The errors found imply that the geometrical distribution of ionization sources may partly account for the large scatter in metallicities derived using model-calibrated empirical methods.