We investigate the distribution of atoms and diatomic metal-oxide molecules in femtosecond-laser-induced plasmas generated at and after the laser beam focal plane, where non-linear phenomena give rise to the formation of a weakly ionized air plasma channel. We use direct plasma imaging and optical emission spectroscopy to study plasma expansion, and the associated physical and chemical separation processes. Plasma splitting occurs upon the interaction of the weakly ionized plasma with the sample and is accompanied by a change in the spatio-temporal distribution of the molecules and atoms compared to sampling at the focus. Furthermore, molecular emission is favored at specific locations and is enhanced over atomic emission as the sample is moved underneath the laser focus. These findings support the ability to enhance or impede the formation of molecular versus atomic species at specific spatio-temporal locations in the laser-induced plasma.