There are trade-offs between cost and capabilities throughout specification, implementation and operation of automated solutions in manufacturing companies. This chapter describes four identified dilemmas or contradictions while balancing flexibility to automation, based on an empirical study with interviews and workshop in five internationally competitive manufacturing companies. The study generated insights on experienced challenges while implementing automated solutions in manufacturing, and these apparent conflicts between automated solutions and maintaining a high operational flexibility need to be managed as manufacturing automation will continue to increase on all levels. © 2017, Springer International Publishing AG.