Alternate bearing exerts economic and environmental consequences through unfulfilled yield potential and fertilizer runoff, respectively. We will discuss a systematic biological–statistical modeling management integration approach to address the concert of mechanisms catalyzing alternate bearing. New engineering technologies (precision harvesting, spatially variable fertigation, and mathematical crop modeling) are enabling optimization of alternate bearing systems. Four years of harvest data have been collected, documenting yield per tree of an 80-acre orchard. These results have shown variability within orchard to range from 20–180 lbs per tree per year. Results indicate irregular patterns not directly correlated to previous yield, soil, or tissue nutrient levels, or pollen abundance. Nor does significant autocorrelation of high or low yields occur throughout the orchard, suggesting that genetically dissimilar rootstocks may have significant impact. The general division of high- and low-yielding halves of the orchard may infer a biotic incongruency in microclimates. This orchard does not display a traditional 1 year-on, 1 year-off cyclic pattern. Delineation of causal mechanisms and the ability to manage effectively for current demands will empower growers to evaluate their fertilization, irrigation, male: female ratio, site selection, and economic planning. In comparison to annual crops, the application of precision agriculture to tree crops is more complex and profitable. When applied in conjunction, the aforementioned methods will have the ability to forecast yields, isolate mechanisms of alternate bearing, selectively manage resources, locate superior individuals, and establish new paradigms for experimental designs in perennial tree crops.