The study of microorganisms and their interactions with polymer matrices represents a key aspect of microbiology and biotechnology. Electron microscopy is an essential tool in this context, as it enables detailed imaging of cell ultrastructure as well as fine polymer networks with high resolution. This dissertation focuses on the development and optimisation of sample preparation methods and imaging strategies that provide the most reliable visualisation of microorganisms and biohybrid materials, with an emphasis on a methodological framework rather than direct application. The first part of the work was dedicated to conventional imaging methods combined with cryogenic fixation of cells, which allowed a comparison of ultrastructural details and provided valuable experience with sample preparation. Building on this, low-voltage transmission and scanning transmission electron microscopy were implemented. These approaches made it possible to visualise both cells and polymer matrices at lower electron energies, while also offering the possibility of imaging without the use of highly toxic uranyl-based staining agents. This represents a promising alternative to commonly used high-voltage techniques, opening the way towards safer and more sustainable imaging strategies. Further experiments were focused on the preparation of model polymer matrices. First, the fixation and stability of agarose hydrogels were tested, serving as a model system for optimising the methodology. Subsequently, protocols were developed and refined for alginate hydrogels containing encapsulated Azotobacter vinelandii cells. The results demonstrated that with properly chosen conditions of gelation and fixation, it is possible to preserve both the fine polymer network and the integrity of microbial cells, enabling detailed ultrastructural studies. Overall, this dissertation provides a comprehensive methodological overview of current possibilities in electron microscopy and biological sample preparation, ranging from conventional and cryogenic approaches to low-voltage imaging and applications in hydrogel systems with encapsulated microorganisms. The outcomes contribute to expanding the toolbox for safer, more efficient, and realistic microscopic studies of biotechnologically relevant microorganisms and their interactions with polymer carriers.