A new approach for design of large-scale manufacture of stem cell derived cells by using the biomechatronic methodology and computer-aided-design tools is described. The systematic conceptual design methodology for systems composed of active mechanical, electronic and biological components, here referred to as biomechatronics, is combined with the methodology for computer-aided design of bioprocesses. The objective has been to systematically investigate and compare by the combination of the methodologies what are favourable design alternatives in terms of equipment configuration and economic parameters. A demonstration case has been used for the manufacture of cardiomyocytes from human induced pluripotent stem cells. The results show how certain configurations are more favourable than others under given boundary conditions. The study indicates that the approach is possible to apply on other related bio-manufacturing systems. (C) 2013 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.