A novel series of Cu(II) complexes with formula M(HLn)(ClO4)2·mH2O [HLn: 13-membered pentaazamacrocyclic ligand resulted from condensation of N,N′-bis(2-aminoethyl)ethane-1,2-diamine, l-tyrosine (HL1)/l-tryptophan (HL2)/l-phenylalanine (HL3) and formaldehyde] were synthesized by one-pot method. Techniques such as ESI–MS, IR, UV–Vis and EPR spectroscopy provided data characterizing the complexes as mononuclear species. The course of thermal decomposition was followed using TG/DSC–MS analysis in air atmosphere. The TG curves showed a gradual decomposition in several stages that comprise dehydration, decomposition of perchlorate ions as well as fragmentation and oxidative degradation of the organic part. The intermediates formed after first stage of water elimination are stable on 40, 15 and 80 °C interval for complexes (1), (2) and (3), respectively. The compounds were tested on the eukaryotic unicellular organism Saccharomyces cerevisiae, showing variable actions in terms of toxicity, cellular uptake and capacity to alleviate growth defects associated with Cu, Zn-superoxide dismutase (SOD1) depletion.