Magnetic fields and stellar spots can alter the equivalent widths of absorption lines in stellar spectra, varying during the activity cycle. This also influences the information that we derive through spectroscopic analysis. In this study, we analyze high-resolution spectra of 211 sunlike stars observed at different phases of their activity cycles, in order to investigate how stellar activity affects the spectroscopic determination of stellar parameters and chemical abundances. We observe that the equivalent widths of lines can increase as a function of the activity index log R_HK_' during the stellar cycle, which also produces an artificial growth of the stellar microturbulence and a decrease in effective temperature and metallicity. This effect is visible for stars with activity indexes log R_HK_'>=-5.0 (i.e., younger than 4-5Gyr), and it is more significant at higher activity levels. These results have fundamental implications on several topics in astrophysics that are discussed in the paper, including stellar nucleosynthesis, chemical tagging, the study of Galactic chemical evolution, chemically anomalous stars, the structure of the Milky Way disk, stellar formation rates, photoevaporation of circumstellar disks, and planet hunting.