Producing high quality protein microarrays on inexpensive substrates like polystyrene is a big challenge in the field of diagnostics. Using a non-contact inkjet printer we have produced microarrays on polystyrene slides for two different biotinylated biomolecules, bovine serum albumin (BSA–biotin) and immunoglobulin-G (IgG–biotin), and studied the influence of buffer (composition and pH) on the spot morphology and signal intensity. Atomic force microscopy revealed the morphological pattern of the (biomolecule) spots printed from phosphate buffer (pH 7.4), phosphate buffered saline (pH 7.4) and carbonate buffer (pH 9.6). The spots showed an irregular crust-like appearance when printed in phosphate buffered saline (pH 7.4), mainly due to the high NaCl content, whereas spots of biomolecules printed in carbonate buffer (pH 9.6) showed a smooth morphology. In addition, the rinsing of these dried spots led to the loss of a considerable fraction of the biomolecules, leaving behind a small fraction that is compatible with the (mono)layer. It was confirmed by confocal laser microscopy that the quality of the spots with respect to the uniformity and distribution of the biomolecules therein was superior when printed in carbonate buffer (pH 9.6) as compared to other buffer systems. Particularly, spotting in PBS yielded spots having a very irregular distribution and morphology.