The objective of the study was to assess the effects of long-term application of liquid manure from pig production and digestate from manure fermentation installation for biogas production on chemical changes in the soil, i.e.: soil reaction, accumulation of available forms of phosphorus, potassium, and magnesium in the soil arable layer, as well as the phosphorus balance. The assessment was carried out in two highly productive farms specialising in pig production, located in the Zachodniopomorskie Province. The soils under the study were treated with slurry and digestate annually for subsequent 12 years. The assessment of changes in nutrient content and accumulation was performed twice: after 10 and 12 years of fertiliser treatments. The rate of changes in soil reaction due to slurry and digestate application varied depending on the analysed field. Irrespective of the analysed field, 12-year application of slurry caused a drop in soil pH by an average of half a unit. The direction of changes in the content of available nutrient forms in the soil varied depending on the element evaluated. Notwithstanding the analysed field and the type of slurry used, a decrease in the content of available forms of potassium in the soil was observed. Slurry fertilisation did not affect magnesium contents in the soil. In the study period, the content of magnesium remained unchanged. Among the evaluated nutrients, an increased nutrient content in the soil was only found in the case of phosphorus – as a result of application of liquid manure in combination with mineral fertilisation. In the analysed farms, in the case of fields fertilised with slurry and digestate, the phosphorus balance was positive, and ranged from 15 to 40 kg P·ha−1. The obtained values of the phosphorous balance strongly suggest that regardless of the type of liquid manure used on the farm, measures should be taken to introduce changes in the scope of fertilisation plans, with particular emphasis on the principles of balanced fertilisation.