An improved impregnation method for ciliates has been described with a new formulation for silver proteinate synthesized in situ, that avoids necessary its long-time laboratory synthesis or use of expensive commercial protargol. Compared to conventional techniques, the proposed protocol is more time-saving, reduces the consumption of chemicals and excludes some hazardous ones (e.g. xylene). Structures that are impregnated such as nuclear apparatus, infraciliature, cortical and cytoplasmic microtubules are stained almost identical compared to other protargol methods. Advantages of this method allow us to merge it successfully with ecological quantitative studies of various natural communities of ciliates and provide correct identification of species during such investigations.