Bacterial communities colonize the surfaces of lichens in a biofilm-like manner. The overall structure of the bacterial communities harboured by the lichens shows similarities, in particular the dominance of not yet cultured Alphaproteobacteria. Parameters causing variation in abundance, composition and spatial organization of the lichen-associated bacterial communities are so far poorly understood. As a first step, we used a microscopic approach to test the significance of both lichen-intrinsic and extrinsic environmental factors on the bacterial communities associated with 11 lichen samples, belonging to six species. Some of these species have thalli with a distinct age gradient. A statistically significant effect can be attributed to the age of the thallus parts, which is an intrinsic factor: growing parts of the lichens host bacterial communities that significantly differ from those of the ageing portions of the thalli. The substrate type (rock, tree, understory) and (at a lower extent) the exposition to the sun also affected the bacterial communities. Interestingly, the abundance of bacterial cells in the lichens was also influenced by the same structure-triggering factors. No effect on the composition with main bacterial groups was attributed to different lichen species, differentiated thallus parts or thallus growth type. Our results are important for the experimental designs in lichen-bacterial ecology.