The recent gamma-ray burst (GRB) GRB 211211A provides the earliest (∼5 hr) data of a kilonova (KN) event, displaying bright (∼1042 erg s−1) and blue early emission. Previously, this KN was explained using simplistic multicomponent fitting methods. Here, in order to understand the physical origin of the KN emission in GRB 211211A, we employ an analytic multizone model for r-process-powered KNe. We find that r-process-powered KN models alone cannot explain the fast temporal evolution and the spectral energy distribution (SED) of the observed emission. Specifically, (i) r-process models require high ejecta mass to match early luminosity, which overpredicts late-time emission, while (ii) red KN models that reproduce late emission underpredict early luminosity. We propose an alternative scenario involving early contributions from the GRB central engine via a late low-power jet, consistent with plateau emission in short GRBs and GeV emission detected by Fermi-LAT at ∼104 s after GRB 211211A. Such late central engine activity, with an energy budget of ∼a few percent of that of the prompt jet, combined with a single red KN ejecta component, can naturally explain the light curve and SED of the observed emission, with the late-jet–ejecta interaction reproducing the early blue emission and r-process heating reproducing the late red emission. This supports claims that late low-power engine activity after prompt emission may be common. We encourage early follow-up observations of future nearby GRBs and compact binary merger events to reveal more about the central engine of GRBs and r-process events.