Vegetation indexes help perform precision farming because they provide useful information regarding moisture, nutrient content, and crop health. Primary sources of those indexes are satellites and unmanned aerial vehicles equipped with expensive multispectral sensors. Reducing the price of obtaining such information would increase the availability of precision farming for small farms. Several studies have proposed deep neural network methods to estimate the indexes from RGB color images. However, these methods report relatively large errors for mature plants when highly non-linear relationships of images and vegetation indexes arise. One could apply multilayer random forest-based models (Deep Forests) to solve this problem, but the discriminative power of such models is limited: they cannot catch complex dependencies between image features. In this paper, we propose a method that combines ideas of deep forests, random forests of kernel trees, and global pruning of random forests to tackle the problem. As a result, the method considers the properties of objects with a complex structure: the presence of relationships between groups of features, displacement, and scaling of objects. The experimental results show that the proposed method outperforms neural network-based solutions in several datasets.