Today's competitive world means conflicting objectives for processes, which are frequently required to perform at the edge of their performance capabilities. In order to cope with such a dynamic environment, commercial companies introduce more flexibility in their processes and systems. Although flexibility may bring benefits such as increased production and product customisation, if not property controlled, it could lead to ineffective decisions, larger inventories, higher costs and customer dissatisfaction, namely to ineffective systems. Adding flexibility to the factory processes increases the decision-making complexity. So far, no global and unifying approach has been offered on manufacturing complexity. The reasons include the variety, dynamism, and uncertainty of the sources of complexity and the relationships between them. It is no longer practical to insist on using well-established rules and procedures to manage process operations and there is a need to re-address and understand the impact of complexities that are present in factories/processes. The problem of managing manufacturing complexities can be stated as understanding the trade-off among costs, service levels and flexibility of responsiveness in manufacturing systems for various strategies under alternative conditions. This paper addresses the issues involved in how to manage manufacturing complexity.