Animal slurry is separated in order to avoid excessive nitrogen, phosphorus and potassium (NPK) fertilization of crops in the field. To enhance fertilizer efficiency further, slurry and its separation products may be acidified, for instance in animal houses. The current study quantified the effects of these treatments, both individually and in combination, on fertilizer efficiency, energy production and heavy metal accumulation as a result of manure management. Acidification increased the availability of N to plants in the manure applied, and provided a better match between plant-available NPK in the manure and separation fraction applied to fields and crop need. Total biogas production was not affected by separation, whereas acidification reduced biogas production because the process was inhibited by a low pH and a high sulphur concentration. The amount of copper applied per hectare in the liquid manure to the wheat field was lower than the amount taken up and more zink and copper was applied in the solid fraction to maize field than taken up. The transportation and field application of solids and liquids did not increase management costs when compared to the transportation of slurry alone, but the investment and running costs of separators and manure acidification increased overall management costs.