Nonlinear physics and agroecosystems can be of great relevance in the synchronisations of chaotic oscillators. The endogenous dynamics of the seed production of perennial plant species which include alternate bearing and masting, portray typical synchronisation patterns in nature and can be modelled using a tent map known as a resource budget model (RBM). This study investigates the collective rhythm in 9,562 pistachio trees caused by their endogenous network dynamics and exogenous forces (common noise). Common noise and a local coupling of RBMs are the two primary factors emerging from the bearing phase synchronisation in this orchard. The in-phase/out-of-phase analysis technique quantifying the strength of the phase synchronisation in trees (population /individual) allows us to study the observed spatial synchrony in detail. We demonstrate how three essential factors, i.e. (a) common noise, (b) local direct coupling, and (c) the gradient of the cropping coefficient, explain the spatial synchrony of the orchard. Here, we also show that the methodology employing nonlinear physics to study agroecological systems can be useful for resolving practical problems in agriculture including yield variability and spatial synchrony which often compromise efficient resource management.