To reduce the cost of silica-based materials, an agricultural waste, rice husk (RH), was transformed into higher valuable products such as MCM-41 and organo-functionalized MCM-41 in the frame of circular economy. RH is the biomass waste containing the highest amount of silica (214 g kg−1). Direct calcination of RH led to silica with low surface area (10 m2 g−1), which could not be transformed into MCM-41. After optimization, silica of 310 m2 g−1 was produced by washing RH with HCl 0.1 mol L−1 at 25 °C and calcination at 600 °C. Such silica was successfully transformed in one-step synthesis at 115 °C for 24 h into highly ordered MCM-41 (800 m2 g−1) and organo-functionalized MCM-41 (510–720 m2 g−1) including aminopropyl and amide derivatives of amino acids (leucine, serine and tyrosine). The corresponding organo-triethoxysilanes alone or in mixture were directly added in the synthesis with silica from RH, octadecyltrimethylammonium and NaOH solution. Surfactant removal was successfully performed with EtOH/NH4NO3 solution at 60 °C. The mesopore diameter of the materials were homogeneous and varied from 3.8 to 4.2 nm depending on the organic functions. Thanks to the use of the concept of pseudomorphic transformation, the particle size of the materials ranged from 1 to 100 μm. As proof of concept, the 50–100 μm fraction (30% of the volume) was successfully used to fill columns to run size exclusion chromatography for protein separation. The largest protein, bovine serum albumine (BSA) was excluded from all materials as its kinetic diameter (d = 7.2 nm) was larger than the mesopore diameter. The smallest proteins: carbonic anhydrase (d = 4.2 nm), myoglobin (d = 3.8 nm) and lysozyme (d = 3.4 nm) were retained by the materials. Their retention factor increased as the kinetic diameter decreased, as the mesopore diameter decreased and as the hydrophobicity of the materials increased. The best separation of proteins was obtained with MCM-41 functionalized with both leucine and serine amide derivatives.