This volume contains the accepted papers at the third Workshop on Membrane Computing and Biologically Inspired Process Calculi, held in Bologna on 5th September 2009. The papers are devoted to both membrane computing and biologically inspired process calculi, as well as to other related formalisms. The papers of this volume are selected by the programme committee due to their quality and relevance; they have defined an exciting programme highlighting interesting problems and stimulating the search for novel ways of describing related biological phenomena. In addition, we had an invited talk given by Luca Cardelli on a spatial process algebra for developmental biology. Membrane systems were introduced as a class of distributed parallel computing devices inspired by the observation that any biological system is a complex hierarchical structure, with a flow of materials and information that underlies their functioning. The emphasis is on the computational properties of the model, and it makes use of automata, languages, and complexity theoretic tools. On the other hand, certain calculi such as mobile ambients and brane calculi work with similar notions (compartments, membranes). These calculi are used to model and analyze the various biological systems. The workshop on Membrane Computing and Biologically Inspired Process Calculi brings together researchers working in these fields to present their recent work and discuss new ideas concerning the formalisms, their properties and relationships.