Due to the environmental and human health concerns of the conventional agricultural practices, organic and biodynamic represent eco-friendly alternative farming systems that increase crop productivity while sustaining soil health. Present study is dedicated to examine the soil fertility as affected by long term application of three different farming systems, bio-dynamic, organic and conventional (DOK). To do that, the rhizosphere soil of wheat plants (W-Rh) grown under DOK farming systems were collected and the total population numbers of bacteria, fungi, diazotrophs, phosphate and potassium solubilizing bacteria were assessed, as well as the chemical and physical properties of W-Rh-soils. To evaluate the bacterial functional capabilities, we obtained a number of bacterial isolates, representing the three farming systems, and characterized their direct and indirect plant growth promoting (PGP) activities. A bioassay test was performed to determine the capacity of DOK soils to support the germination and growth performance of wheat plant. The results revealed that D-W-Rh samples harbored significantly higher bacterial populations in comparison to O-W-Rh and K-W-Rh samples, whereas the opposite pattern was observed for fungal populations. Bacterial isolates from the three systems exhibited diverse capabilities, without a clear correlation between a specific function with a particular system. Bioassay test revealed that wheat plants grown in soil form biodynamic system displayed higher germination rate, root and shoot fresh and dry weights followed by those from organic then conventional systems. Thus, different systems had distinct impacts on soil fertility with the biodynamic having a superior influence on the measured plant growth parameters.