Tropical instability vortices (TIVs) in the equatorial Pacific exhibit energetic horizontal and vertical circulation characterized by regions of high Rossby number and low Richardson number. Their strong anticyclonic vorticity and vertical shear can influence the broader-scale circulation by driving lateral mixing and vertical exchange between the ocean surface and interior. The authors use a set of nested high-resolution simulations of the equatorial Pacific, with a finest grid size of 3 km, to examine the vortex dynamics associated with TIV core water formation. TIV cores are characterized by low values of the Ertel potential vorticity (PV) as the relative vorticity is anticyclonic with magnitude comparable to the local Coriolis parameter. A study of the variation of PV and other scalars along Lagrangian fluid parcel tracks entering the TIVs shows that the low-PV water in their cores is a mix of Equatorial Undercurrent (EUC) water and North Equatorial Counter Current (NECC) water. The EUC water is characterized by strong horizontal vorticity, and thus, the baroclinic component of the PV is nonnegligible and acts as a source for the anticyclonic vorticity of TIVs. This horizontal vorticity is tilted by an ageostrophic secondary circulation associated with strain-induced frontogenesis that tends to form along the path of the EUC water that enters the vortex. Frontogenesis disrupts the cyclogeostrophic balance of the frontal flow and drives differential vertical motions across the front. These results emphasize the role of submesoscale physics in the equatorial region, which are active when both the Rossby and Richardson numbers are O(1).