A search for flavor-changing neutral-current couplings between a top quark, an up or charm quark and a $Z$ boson is presented, using proton-proton collision data at $\sqrt{s} = 13$ TeV collected by the ATLAS detector at the Large Hadron Collider. The analyzed dataset corresponds to an integrated luminosity of 139 fb$^{-1}$. The search targets both single-top-quark events produced as $gq\rightarrow tZ$ (with $q = u, c$) and top-quark-pair events, with one top quark decaying through the $t \rightarrow Zq$ channel. The analysis considers events with three leptons (electrons or muons), a $b$-tagged jet, possible additional jets, and missing transverse momentum. The data are found to be consistent with the background-only hypothesis and 95% confidence-level limits on the $t \rightarrow Zq$ branching ratios are set, assuming only tensor operators of the Standard Model effective field theory framework contribute to the $tZq$ vertices. These are $6.2 \times 10^{-5}$ ($13\times 10^{-5}$) for $t\rightarrow Zu$ ($t\rightarrow Zc$) for a left-handed $tZq$ coupling, and $6.6 \times 10^{-5}$ ($12\times 10^{-5}$) in the case of a right-handed coupling. These results are interpreted as 95% CL upper limits on the strength of corresponding couplings, yielding limits for $|C_{uW}^{(13)*}|$ and $|C_{uB}^{(13)*}|$ ($|C_{uW}^{(31)}|$ and $|C_{uB}^{(31)}|$) of 0.15 (0.16), and limits for $|C_{uW}^{(23)*}|$ and $|C_{uB}^{(23)*}|$ ($|C_{uW}^{(32)}|$ and $|C_{uB}^{(32)}|$) of 0.22 (0.21), assuming a new-physics energy scale $\Lambda_\text{NP}$ of 1 TeV.