Aims: The aim of this study was to evaluate the effects of long-term mineral and organic fertilisation on crop performance and soil fertility. Methods: The Long-Term Nutrient Depletion Trial (Denmark) was used to analyse changes in concentrations of Olsen-P, exchangeable potassium (K) and soil carbon (C). Yield responses (2010–2016) were evaluated making use of an early-season temperature model, fertilisation practices were evaluated by nutrient budgets, and nitrogen use efficiency by calculation of apparent recovery (ANR) in subplots receiving mineral N. Results: Olsen-P (r² = 0.68, P < 0.001) and exchangeable K (r² = 0.86, P < 0.001) were correlated with the nutrient budgets. Soil C concentrations increased from 10.0 g kg⁻¹ (1995) to between 11.1–14.6 g kg⁻¹ (2016), with the greatest accumulation under slurry applications (P < 0.05, equalling 17–47% retention of slurry-C inputs). Relative yield responses of spring barley were associated with early season cold stress, but the model was not applicable to other crops. Increases of ANR in response to long-term phosphorus (P) applications were not significant. Conclusions: Balanced fertilisation is an effective way to maintain nutrient availability, and to ensure high and stable crop productivity and efficient use of nutrients. Direct C inputs from animal slurry are a major driver for increases of soil C concentrations.