Over time fouling leads to membrane wetting. This is the biggest obstacle to widespread use of membrane distillation (MD) for ammonia removal from animal slurry. Feed pretreatment and cleaning strategies of membrane surfaces are the most common methods to prevent or diminish fouling phenomena. This study investigates preliminary fouling of polypropylene (PP) and polytetrafluoroethylene (PTFE) membranes. A model manure solution was used as feed. In addition cleaning efficiencies with deionized water, NaOH/citric acid, and Novadan agents were studied. Further microfiltration and ultrafiltration were examined as manure pretreatment to diminish fouling. To this end polyvinylidene fluoride membranes (PVDF 0.2 µm and 150 kDa respectively) were used. Organic fouling was shown to be dominant. For the model manure solution the fouling comprised lipids, carbohydrates and proteins. For pig slurry the fouling additionally contained carboxylates, free fatty acids and lignin. Among the tested cleaning strategies, Novadan agents were the most successful in removing proteins and carbohydrates from the PTFE membrane while it only removed proteins from the PP membrane. Using microfiltration or ultrafiltration as a pretreatment prior to MD doubled the ammonia mass transfer coefficient for the PTFE membrane, while for the PP membrane, the ammonia mass transfer coefficient was increased 4-fold.