Operative planning in agricultural production has historically had the objective of improving yields and quality. Sowing, cropping, and harvesting are usually treated independently, and waste and the sustainability of operations are generally not integrated into operational planning methodologies for agricultural production. This study shows the need to have a clear and precise methodology to minimize waste in agricultural production systems to ensure sustainability. This need is addressed with a novel methodological guide to minimizing waste in agricultural operations, crop maintenance, and harvesting. The proposed methodology is founded on the use of lean manufacturing as a waste-management tool. Lean manufacturing principles allow agricultural operations and the variables that represent wastes to be identified, mathematical models to be built, constraints to be defined, and the cost of waste to be illustrated, as well as its minimization through an objective function. To guide implementation, we propose a conceptual model to explain the construction of a mathematical model that represents the development of decision variables on agricultural operations with the elements to consider and the constraints and theoretical proposal of the necessary objective function. The proposed conceptual model and the constructed methodology constitute a novel development within agricultural production systems that could be used by decision makers and farmers. © 2019 Society of Chemical Industry.