The first stage in the precision agriculture cycle has been a vital study area in recent years because it allows soil testing followed by data analysis. In this stage, a strategic delineation of site-specific management zones acquires a particular interest because it enables site-specific treatment to improve crop yield by efficiently using the input of resources. The delineation of site-specific management zones problem is to determine the minimum number of zones that cover the entire field so that each zone’s homogeneity is significant according to a specific biological, chemical, or physical soil property. Furthermore, the delineated zones should be orthogonal-shaped to be practical for agricultural machinery. This work has proposed a new bio-inspired algorithm, specifically an Estimation of Distribution Algorithm, based on a decoder that heavily relies on the Disjoint-Set algorithm and a new reactive penalized fitness function that detects unfeasible solutions. The new methodology improves the solutions presented in the literature by using a new search engine that drastically reduces the computational times of similar algorithms. Our algorithm has been tested with the literature benchmark, considering a new reactive penalization in the fitness function. It obtains the best solutions for 66.66% of the instances benchmark compared to the best literature method. Due to the algorithm’s efficiency, a new set of larger instances is introduced to test the scalability and robustness of the method. It obtained an efficiency of 79.3%.