Non-equilibrium cold atmospheric plasmas (CAPs) are, starting with the discovery of ozone production in a silent discharge by Werner von Siemens in the year 1857, the longest serving man-made plasmas in the history of the human race. They can generate high densities of reactive and internally excited species at very low or moderate gas temperatures, which can be utilized in many surface treatment processes. They can effectively charge surfaces, which resulted in application in dust precipitators or photocopiers, or they can emit photons in the ultraviolet and vacuum ultraviolet range, which is very effectively used in plasma displays. The low gas temperature and the atmospheric pressure operation make them attractive for the surface processing of materials and very friendly to many non-standard substrates such as fabrics, wood, liquids, or even living tissues. Several special issues in this journal have already been dedicated to CAPs: two special issues devoted to Plasma Medicine in years 20081 and 2010,2 a Cold Atmospheric Plasma issue in 2008,3 the special issue “Highlights from the 10th International Symposium on High Pressure, Low Temperature Plasma Chemistry” published in 20074 and a Plasma Sterilisation and Decontamination issue in this year3 with several contributions presenting effects of CAPs.5 This demonstrates the growing interest of the plasma-science community in this type of technology. This interest is, however, accompanied by the awareness of the intrinsic limitations of CAPs. Very high collisional rate and several instabilities lead to preferential filamentation of the plasma. Homogeneous discharge is usually achieved only under very limited range of process parameters, in confined volumes (microplasmas) and/or with special design of both the plasma source and the power supply. Additionally, due to the atmospheric operation, collisional sheaths prevent ion bombardment of the surface and frequent collisions lead also to fast cluster formation. All this limits the application of CAPs for large-scale deposition of high quality and homogeneous thin films or for anisotropic etching and they will very probably never replace low-pressure plasmas in these areas. On the other hand, and this double special issue is a convincing argument for it, there are still many exciting and often unexplored areas, where the CAPs can be used successfully for material synthesis in the gas phase, liquid phase and at the surface. The purpose of this special issue is to show recent progress in this multifaceted field by many of the most distinguished plasma-scientists and provide the overview for somebody who wants to start the research or is looking for plasma application in this area. In this special issue, one review article and three feature articles provide the state-of-the-art and identify key future challenges of the CAP deposition of thin films by dielectric barrier discharges and microplasmas, as well as of nanoparticles synthesis and functionalization by microplasmas in the liquid phase. Moreover, this special issue includes another eight full articles covering the topics from the deposition of coatings for biomedical interest, over the fundamental studies of SiO2 film deposition mechanism, to the synthesis of membrane-electrode assembly for fuel cells and the deposition in microfluidic channels. The issue also contains three original contributions on the continually growing area of nanomaterials production such as the synthesis of silica nanowires, carbon nanotubes or metal nanoparticles. We, the guest editors, are very happy that we could with this special issue attract so much interest from all the authors, and we thank them very much for their excellent contributions. Our thanks go also to all reviewers for their valuable time and effort in securing the highest scientific standards possible. We would like to express our sincere gratitude to the Editors-in-Chief for offering us the privilege to prepare this special issue and to the Managing Editor Dr. Renate Förch for helping us with its coordination.