This paper reports the first systematic investigation on the effects of atmospheric-pressure helium microplasma array treatment on the surface chemistries of model organic materials and a biological coating. These materials include polystyrene (PS), low-density polyethylene (LDPE) and ethylene tetrafluoroethylene (ETFE), and bovine serum albumin (BSA). The plasma treatment introduced a range of oxygen functionalities into the surface of the polymers, with oxygen incorporation reaching “saturation” after relatively short treatment times. PS and LDPE surfaces were more readily oxidised and to a greater depth compared to ETFE. The polymer surfaces became smoother at short plasma treatment times due to removal of adventitious hydrocarbon, but became rougher at longer treatment times as a result of etching of low molecular weight, volatile material from the surface. Atmospheric-pressure helium microplasma array treatment of a BSA layer resulted in the majority of the protein being removed from the underlying (PS) surface. The plasma treatment reduced the surface roughness of the BSA coating at short treatment times, but at longer treatment times, the surface roughness increased and the surfaces exhibited granular structures. All of the hydrophobic polymers became hydrophilic after the plasma treatment. The hydrophilicity of the surfaces decreased upon storage (hydrophobic recovery) and none of the polymers reverted to their original hydrophobic state, even after 500 h of storage. The knowledge presented in this paper may be useful in the development of new manufacturing processes based on atmospheric-pressure plasma and in the field of plasma medicine, particularly with respect to cleaning and sterilisation methods. In addition, it provides a foundation for future efforts to establish the mechanisms behind interactions of atmospheric-pressure plasmas with materials.