In microproduction, i.e. in the production and assembly of micro-scale components and products, fully automated systems hardly exist so far. Besides the requirements of handling small parts with extreme precision, small batch sizes of highly customized products are among the main challenges. Therefore, economic microproduction requires very flexible production systems with a high level of automation. This contribution proposes a new concept of such a system that provides two main innovations. First, the proposed concept integrates stationary production machines and mobile transport robots in order to configure rapidly changing production processes in real-time. Besides this distributed flexible system structure, also the overall automation system consisting of the Manufacturing Execution System (MES) and the shop floor control is designed in a distributed form as a multiagent system. This distributed automation system is especially suited to automate flexible production scheduling and resource allocation processes but also integrates the multi-robot transport system. © 2013 IEEE.