This book constitutes the proceedings of the 12th European Conference on Modelling Foundations and Applications, ECMFA 2016, held as part of STAF 2016, in Vienna, Austria, in July 2016. The 16 papers presented in this volume were carefully reviewed and selected from 47 submissions. The committee decided to accept 16 papers, 12 papers for the Foundations Track and 4 papers for the Applications Track. Papers on a wide range of MBE aspects were accepted, including topics such as multi- and many models, language engineering, UML and meta-modeling, experience reports and case studies, and variability and uncertainty.