The vulnerability of buildings and structures to rain and flooding due to a lack of adaptive capacity is an issue all over the world. Exploring the bio-resources availability and engineering performance is crucial to increase infrastructure’s resilience. The current study analyses earth-based mortars using mineral precipitation as a biostabiliser (bio) and compares their performance with cement-based mortars. Cultures of S. oneidensis with a concentration of 2.3 × 108 cfu/mL were used to prepare earth-based and cement-based mortars with a ratio of 6% of binder. Microstructure analyses through SEM/EDS, water absorption, moisture buffering, mechanical strength, and porosity are discussed. The biostabiliser decreases water absorption in tidal-splash and saturated environments for earth and cement mortars due to calcium carbonate precipitation. The biostabiliser can prevent water migration more effectively for the cement-based (60% reduction) than for the earth-based mortars (up to 10% reduction) in the first 1 h of contact with water. In an adsorption/desorption environment, the conditions favour desorption in cem+bio, and it seems that the biostabiliser precipitation facilitates the release of the chemicals into the mobile phase. The precipitation in the earth+bio mortar porous media conditions favours the adsorption of water molecules, making the molecule adhere to the stationary phase and be separated from the other sample chemicals. The SEM/EDS performed for the mortars confirms the calcium carbonate precipitation and shows that there is a decrease in the quantity of Si and K if the biostabiliser is used in cement and earth-mortars. This decrease, associated with the ability of S. oneidensis to leach silica, is more impressive for earth+bio, which might be associated with a dissolution of silicate structures due to the presence of more water. For the tested earth-based mortars, there was an increase of 10% for compressive and flexural strength if the biostabiliser was added. For the cement-based mortars, the strength increase was almost double that of the plain one due to the clay surface negative charge in the earth-based compositions.