We propose an scenario to study, from a dynamical point of view, the thermal recombination of quarks in the midsts of a relativistic heavy-ion collision. We coin the term dynamical quark recombination to refer to the process of quark-antiquark and three-quark clustering, to form mesons and baryons, respectively, as a function of energy density. Using the string-flip model we show that the probabilities to form such clusters differ. We apply these ideas to the calculation of the proton and pion spectra in a Bjorken-like scenario that incorporates the evolution of these probabilities with proper time and compute the proton to pion ratio, comparing to recent RHIC data at the highest energy. We show that for a standard choice of parameters, this ratio reaches one, though the maximum is very sensitive to the initial evolution proper time.