One of the important objectives of supply chain S&OP (Sales and Operations Planning) is the profitable alignment of customer demand with supply chain capabilities through the coordinated planning of sales, production, distribution, and procurement. In the make-to-order manufacturing context considered in this paper, sales plans cover both contract and spot sales, and procurement plans require the selection of supplier contracts. S&OP decisions also involve the allocation of capacity to support sales plans. This article studies the coordinated contract selection and capacity allocation problem, in a three-tier manufacturing supply chain, with the objective to maximize the manufacturer's profitability. Using a modeling approach based on stochastic programming with recourse, we show how these S&OP decisions can be made taking into account economic, market, supply, and system uncertainties. The research is based on a real business case in the Oriented Strand Board (OSB) industry. The computational results show that the proposed approach provides realistic and robust solutions. For the case considered, the planning method elaborated yields significant performance improvements over the solutions obtained from the mixed integer programming model previously suggested for S&OP.