In this work, we developed, applied and validated on-site microbiological procedures to study the unique silica stromatolite-like structures present in orthoquartzite caves on venezuelan tepuis. The results prove them as promising terrestrial astrobiological analogues, validate the feasibility of real-time microbial analyses in remote caves and provide novel understanding on the microbiological aspects involved in the formation of silica stromatolites in non-thermal and aphotic environments.