Layer-by-layer (LbL) deposition of poly(L-lysine) (PLL) dissolved in different solutions and a water-soluble titania precursor, titanium(IV) bis(ammonium lactate) dihydroxide (TiBALDH) to form multilayer films on the wall of polycarbonate (PC) membrane pores was performed to prepare nanostructured titania-PLL composite and pure anatase and rutile titania tubes. A battery of analytical techniques was utilized to characterize and compare the structures, crystal phases, and photocatalytic properties of the titania tubes. In different solutions conditions, PLL which adopts secondary conformations (i.e., alpha-helix and random coil) and has varying interactions with different counterions (i.e., chloride and phosphate ions) can influence PLL/TiBALDH deposition and, in turn, results in the titania materials with different nanostructures and phtocatalytic properties. The influence of LbL assembly condition, deposition cycle, and polypeptide molecular weight on photocatalytic properties of resultant anatase titania tubes were further explored and these materials are promising photocatalyst with the advantage of easily handling and recycling. This reported approach may provide a facile and general way to prepare organic-inorganic composite and other inorganic materials with different compositions, structures, and properties for various applications.