Low-cost materials and low-tech architectures could give competitive advantage in scaling-up applications of microbial fuel cells (MFC), especially for nutrients recovery from wastewater. Here a novel concept is presented, based on cylindrical ligno-cellulosic materials, available as agricultural residues or spontaneous vegetation. Giant canes (Arundo Donax L.) and maize (Zea Mays) stalks were used as porous separators (naturally tubular) for air-cathode MFC modules (GC-MFC and MS-MFC, meaning Giant Cane and Maize Stalk, respectively), with carbon cloth-based electrodes. The MFCs were operated across 100 Ω external load, enriching swine-farming wastewater with addition of sodium acetate (3 g L−1). Initially, these systems showed relatively high internal resistances (especially GC, with Rint = 5600 Ω), before the material was completely imbibed by the anolyte. After 10–20 days acclimation, despite sufficient electrolytic conductivity was established in both systems (internal resistance around 60–90 Ω), relatively low power densities (around 40 mW m−2, normalized by cathode's surface projection) were achieved, if compared to state-of-the-art MFCs, oriented to electricity harvesting. However, the generated electric field was enough to sustain electro-osmotic ions mobility and to establish high pH conditions (pH 11–12) at the cathode. Over 70 days of operation, electro-migration and deposition phenomena of valuable elements (Na, Ca, Mg, Mn, K, etc.) were observed, both inside the separator and on the cathode surface. Simultaneously, partial biodegradation of the ligno-cellulosic biomass, especially for MS, drove partial release of organic carbon, nitrogen, phosphorous and other elements in the anodic chamber. These relevant phenomena have to be taken into account in view of possible applications of ligno-cellulosic materials in MFC-driven nutrients recovery from wastewater.