This paper presents material and technological studies on lab-on-chip (LOC) devices as a first step towards biocompatible and reliable research on microscopic fungi and soil organisms on a microscale. This approach is intended to respond to the growing need for environmental control and protection, by means of modern, miniaturized, portable and dependable microfluidics instrumentation. The authors have presented herein long-term, successful cultivation of different fungi representatives (with emphasis put on Cladosporium macrocarpum) in specially fabricated all-glass LOCs. Notable differences were noted in the development of these creatures on polymer, polydimethylosiloxane (PDMS) cultivation substrates, revealing the uncommon morphological character of the fungi mycelium. The utility of all-glass LOCs was verified for other fungi representatives as well – Fusarium culmorum and Pencilium expansum, showing technical correspondence and biocompatibility of the devices. On that basis, other future applications of the solution are possible, covering, e.g. investigation of additional, environmentally relevant fungi species. Further development of the LOC instrumentation is also taken into consideration, which could be used for cultivation of other soil organisms and study of their mutual relationships within the integrated microfluidic device.