Theaflavins (TFs) contribute greatly to the colour and flavor of black tea, and have various bioactivities beneficial to human health. This research compared the activity for enzymatic production of TFs from tea polyphenols by recombinant polyphenol oxidase (Malus domestica, GenBank login number LT718523.1, MdPPO2) versus commercial enzyme (Agaricus bisporus, AbPPO) in both free and immobilized form. It describes the difference in activity for TFs production between recombinant and natural polyphenol oxidase. Enzyme assays by LC-MS revealed that the TFs production by AbPPO was almost 5 times as high as recombinant MdPPO2 in free enzyme. When immobilized on mesoporous silica, the activity of recombinant MdPPO2 increased significantly, while AbPPO almost lost its activity. By comparing relative enzyme activity, the immobilization of recombinant MdPPO2 has the highest relative enzyme activity, which was above 6 times higher than free AbPPO. Among these TFs, TF3 was the most abundant, followed by TF2a, TF1 and TF2b.