Recombinant Escherichia coli based on Pseudomonas fluorescens N3 naphthalene dioxygenase (NDO) was used in two liquid phase bioconversions to produce 1,2-dihydro-1,2-dihydroxy naphthalenes derived from substituted naphthalenes. Five different organic phases (dodecane, silicon oil CR100, dioctyl phthalate, 1-dodecanol, 2-undecanone) were used at different ratios with respect to water and containing different substrate concentrations. The results show different phase effects in terms of both rates and other experimental variables. The differences between substrates are very interesting, showing rate increases from 0.9 to 4 times. The choice of the phase to some extent depends on the substrate, but dodecane shows to be a general effective phase for all the substrates.