The effects of adjusting the initial carbon to nitrogen (C:N) ration and pH of pig manure and straw mixes on ammonia emissions and pathogen marker inactivation during composting were investigated by experimentation and modelling. Three, 210-litre reactors were designed and built to control conditions, such as the maximum operating temperature, minimise temperature gradients and enable analysis of the off-gas for ammonia, water, oxygen and carbon dioxide. Respirometry showed that the optimal temperature for composting pig manure was about 60°C. A simulation model suggested that ammonia emissions could be reduced by lowering the initial pH and increasing the initial C:N ratio of the organic material. Experimentally, lowering the initial pH significantly reduced ammonia emissions. The effect of the initial C:N ratio on ammonia emissions was not significant because of variations in the pig manure. Pathogen markers were sometimes detected after composting from experiments with low ammonia emissions, so questioning the established criteria for pathogen inactivation. Experimental data validated the model, which simulated organic material decomposition using first order reaction rate kinetics and predicted the temperature and ammonia emissions profiles from initial conditions.