Agri-environmental indicators such as nutrient balance may play a key role in soil and water quality monitoring, although short-term experiments might be unable to capture the sustainability of cropping systems. Therefore, the objectives of this study are: (i) to evaluate the reliability of long-term experimental N and P balance estimates to predict real field (RF) (i.e., short-term transitory) conditions; and (ii) to compare the sustainability of short- and long-term experiments. The LTE-based predictions showed that crops are generally over-fertilised in RF conditions, particularly maize. Nutrient balance predictions based on the LTE data tended to be more optimistic than those observed under RF conditions, which are often characterised by lower outputs; in particular, 13, 44, and 47% lower yields were observed for winter wheat, maize, and soybean, respectively, under organic management. The graphical evaluation of N and P use efficiency demonstrated the benefit of adopting crop rotation practices and the risk of nutrient loss when liquid organic fertiliser was applied on a long-term basis. In conclusion, LTE predictions may depend upon specific RF conditions, representing potential N and P use efficiencies that, in RF, may be reduced by crop yield-limiting factors and the specific implemented crop sequence.