The enzymatic polymerization of rutin has been proved as an efficient method for obtaining products with enhanced properties, but toxic organic co-solvents are often involved in this process. In this work, the effect of temperature and enzyme activity were initially studied on 24 h batch oligomerization reactions in organic-free reaction media. The optimal conditions, 1000 U/L and 25 °C, were chosen to operate an ultrafiltration enzymatic membrane reactor (UF-EMR) during three consecutive oligorutin synthesis cycles of 6 and 24 h, with the objective of reusing the initial laccase activity. The use of this technology led to the design of a biocompatible and sustainable process with complete rutin conversion and remarkable laccase stability in at least three consecutive 24 h cycles with no further enzyme addition. Despite an approximately 80% lower ferric reducing antioxidant power (FRAP), oligorutin displayed up to 1620-fold aqueous solubility and 24-fold iron chelating activity. Additionally, tests involving DNA degradation inhibition in exposure to biologically related radicals showed a better performance of oligorutin when compared to rutin.