Recent experiments to fossilise microorganisms using silica have shown that the fossilisation process is far more complex than originally thought; microorganisms not only play an active role in silica precipitation but may also remain alive while silica is precipitating on their cell wall. In order to better understand the mechanisms that lead to the preservation of fossilised microbes in recent and ancient rocks, we experimentally silicified a Gram-positive bacterium, Geobacillus SP7A, over a period of five years. The microbial response to experimental fossilisation was monitored with the use of LIVE/DEAD staining to assess the structural integrity of the cells during fossilisation. It documented the crucial role of silicification on the preservation of the cells and of their structural integrity after several years. Electron microscopy observations showed that initial fossilisation of Gram-positive bacteria was extremely rapid, thus allowing very good preservation of Geobacillus SP7A cells. A thick layer of silica was deposited on the outer surface of cell walls in the earliest phase of silicification before invading the cytoplasmic space. Eventually, the cell wall was the only recognisable feature. Heavily mineralised cells thus showed morphological similarities with natural microfossils found in the rock record.