Although post-weaning mortality (PWM) in pig farming is mainly due to the effect of pathogens, farm type or swine management are also directly or indirectly involved. In this work, we used null models and the partial least squares approach (PLS) to structural equation modelling, also known as PLS path modelling (PLS-PM), to explore whether farm type, swine management and pathogens, including porcine circovirus type 2, swine influenza virus, porcine reproductive and respiratory syndrome virus and Aujeszky's disease virus, directly or indirectly influenced PWM in 42 Spanish indoor pig farms. The null model analysis revealed that contact with multiple combinations of viruses could occur by chance. On the other hand, PLS-PM showed that farm characteristics do not influence virus infections, and thus neither farm type nor associated management practices shaped PWM due to pathogens. Accordingly, preventive programmes aimed at controlling PWM in intensive farming should prioritize the control of major pig pathogens.