Soil fertility is typically assessed by chemical analysis, which is expensive and time-consuming, and hence impractical for site-specific fertilizer management. Visible and near infrared (Vis-NIR) spectroscopy has been used for determining soil properties and chemically extractable plant nutrients. However, the suitability of Vis-NIR for accurate assessment of nutrient availability to plants has not yet been fully explored. In this work, we examined the accuracy of this technique as a new nutrient availability index, and in the case of P as a proxy for plant-available P. To this end, total plant-available P in soil was quantified in a P-depletion experiment with crops, and the availability of Ca, Mg, K, and Fe was assessed by chemical extraction. Vis-NIR spectroscopy allowed us to accurately estimate plant-available P, which depends not only on soil factors but also on the crop performance to take up P. Vis-NIR spectroscopy proved effective in identifying P, Ca, Mg, K, and Fe responsive sites. Precise estimation of plant-available P was a result of accurately predicting soil properties governing P availability to plants by Vis-NIR spectroscopy. In addition, this technique provided accurate predictions of soil properties influencing the dynamics of applied P and K fertilizer, which can be useful to adapt fertilization practices to soil properties. Vis-NIR spectroscopy can therefore enable a qualitative leap to cost-effective integral assessment of soil fertility by providing accurate predictions of soil functioning rather than mere estimates of availability indices, thereby facilitating more sustainable use of resources in agriculture.