Red beetroot extract is a widely used food colorant. Betalain is the major red pigment present in it, which is unstable at high temperature and pH. In this study, the edge of nanoemulsion over microemulsion in improving the thermal and pH stability of betalain has been demonstrated. The micro- and nanoemulsions of beet extract were prepared by rotor-stator homogenization and rotor-stator homogenization followed by ultrasonication, respectively. The resultant emulsions were compared for their physicochemical and rheological properties, storage stability (for 15 days, at refrigeration temperature: 4 ± 1 °C; room temperature: 30 ± 5 °C; 40 °C and 100 °C), and release kinetics. Compared to microemulsion, nanoemulsion resulted in a sustained release and higher thermal and pH stabilities of betalain. During storage, nanoemulsion showed a lower rate of droplet coarsening and improved color stability than microemulsion, due to its nanoscale droplet diameter (701.53 ± 27.2 nm), high viscosity (0.089 Pa s, at 100 s−1), and non-Newtonian rheological behavior.