Iron oxide and silica‐based materials have emerged as attractive protein purification and immobilization matrices. His6 has been reported as an effective affinity tag for both iron oxide and silica. Here, the silica‐binding tags CotB1p and Car9 were shown to work as effectively as iron oxide‐binding tags. Using EGFP as a model protein, commercially available bare iron oxide (BIONs) or silicon dioxide (BSiNs) nanoparticles as low‐cost purification/immobilization matrices, and non‐hazardous and mild binding and elution conditions, adsorption and desorption studies were performed with lysates from Escherichia coli‐producing cells to compare the performance of these dual‐affinity tags. Under the conditions tested, the His6 tag stood out as the best‐performing tag, followed by CotB1p. Our findings concluded the promising combination of these tags, BIONs and BSiNs for one‐step purification of recombinant proteins, and two‐step purification and immobilization of recombinant proteins without intermediate buffer exchange. This proof of concept work set the ground for future evaluation of these purification and immobilization strategies using other proteins with different properties, which will be of interest to expand their utility and applicability.