Periphyton is a valuable, environmentally benign resource widely used in environmental remediation. A protocol for reusing agro-wastes to improve the metabolic activity and versatility of periphyton was tested in this study. Peanut shell (PS), decomposed peanut shell (DPS), acidified peanut shell (APS), rice husks (RHs), acidified rice husks (ARHs), and a commonly used synthetic carrier, ceramsite (C), were used to support periphyton attachment and growth. The results show that the modified carriers have more hydrophilic groups, higher periphyton biomass, and autotrophic indices than the unmodified carriers. As a consequence, they promote the metabolic versatility of periphyton microbial communities. Thus, the periphyton attached to modified agro-wastes (DPS, APS, and ARH) grew in a stable and sustainable manner. This study suggests that modified PS and RH are effective and environmentally benign carriers that enhance periphyton activity and functionality. Development of periphytic carriers using agro-wastes is also a sustainable method of reusing these materials.