Nanotechnology plays an important role in many fields of science and the economy. A special example of nanostructures is silver nanoparticles (AgNPs) created following the principles of green chemistry, i.e., without the use of toxic reducing compounds. The common tomato (Solanum lycopersicum) is a popular vegetable whose germination and growth process are studied by using, e.g., in vitro cultures. The aim of the experiment was to evaluate the inhibitory effect of the biodegradable gels containing silver nanoparticles on the development of microbial infection and to evaluate their influence on the germination degree of Tomato (Solanum lycopersicum) seeds in in vitro plant cultures. Based on macroscopic and microscopic observations, all experimental samples showed the presence of Gram-positive bacilli as well as mould fungi of the genus Rhizopus, Alternaria and Aspergillus. The study showed that the biocomponents containing silver nanoparticles obtained by using xylose as a reducing agent limit the development of microbial infection and stimulate the germination rate of tomato seeds. They could find their application as biodegradable raw materials in the production of modern disinfecting preparations for research in in vitro cultures. This study allowed to identify new research directions, especially to evaluate the metabolic regulation of seedlings treated with biodegradable silver nanoparticles.