[MnCl2(NOR)(H2O)2] (1), [MnCl2(SPAR)(H2O)2] (2), [CoCl2(NOR)(H2O)2] (3) [CoCl2(SPAR)(H2O)2] (4), [CuCl2(phen)(NOR)] (5) and [CuCl2(phen)(SPAR)] (6) complexes with norfloxacin (NOR) and sparfloxacin (SPAR) were obtained from MnCl2·4H2O, CoCl2·4H2O and CuCl2(phen). In all cases the NOR and SPAR coordinate in the neutral zwitterionic form. The electron paramagnetic resonance spectra of the Cu(II) complexes (5) and (6) in aqueous and DMSO solutions indicate mixture of mononuclear and binuclear complex. Complexes (1–6), together with the corresponding ligands were evaluated for their in vitro trypanocidal effect, against both bloodstream trypomastigotes and intracellular forms of Trypanosoma cruzi. SPAR and NOR were poorly effective upon T. cruzi, complexes (3) and (4) were active against intracellular forms of the parasite. The complexes (5) and (6) displayed a higher activity upon both bloodstream and intracellular forms. The potency of fluoroquinolones, specially those coordinated to Cu(II)–phen justify further trypanocidal screening assays with this compounds in vitro as well as upon experimental models of T. cruzi infection.