In this paper a modelling and control structure for product quality control is presented for a class of operations that processes agro-material. This class can be characterised as climate-controlled operations, such as storage, transport and drying. The basic model consists of three parts. These are the quality and behaviour of the product, and its direct and indirect environment. This decomposition is reflected in the proposed control structure. The significance of the explicit inclusion of product behaviour is that the control is much more geared to the demands of the product. The applicability and potential advantages of the proposed structure are illustrated in different industrial cases, such as the storage of potatoes and the transport of apples in reefer-containers.