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BACKGROUND: In managing apple orchards, crop load and rate of nitrogen (N) fertilisation are two factors with a significant influence on fruit quantity and quality, because they affect all physiological processes in the tree. Both factors are strongly related to external and internal fruit quality, especially to skin colour, sugar and acid contents and mineral composition, and consequently to the keeping quality of fruits. The aim of this study was to assess the effects of both factors (three crop load levels and two N fertilisation levels) on the colour development of Golden Delicious apples during the last month on the tree in two consecutive seasons. Data on skin colour (L*, a*, b* values) were analysed using nonlinear mixed effects modelling to extract information on the variation in biological shift factor for colour and to link this variation to the different strategies used concerning N fertilisation and crop load. RESULTS: The major source of information is contained in the a* value. The behaviour of the a* value could be described by a logistic or an exponential model depending on the season and the experimental set-up. Nonlinear mixed effects analysis estimating the biological shift factor (maturity) for each individual fruit (random effect) while estimating the rate constant of the decolouration process in common (fixed effect) resulted in explained parts well over 95%. CONCLUSION: The variation in maturity stage between individual fruits is large. Season has the most profound effect on the estimated values, far more important than that of crop load or fertilisation level. The magnitude of variation in colour due to crop load and N fertilisation is not too large. Its effect on the maturity stage of fruits is more profound: the higher the crop load, the higher the variation. The effect of fertilisation seems to be opposite: the higher the fertilisation level, the lower the variation.