Electron density and Neutral Wind (ENWi) probe and/or Langmuir probe were flown on three different rocket flights from equatorial station Thumba (8.5°N, 77°E), during daytime, eclipse time, and post sunset time respectively, of low solar activity period, to study ionization irregularities in the E region of the ionosphere. The spectral characteristics observed using the payloads were analyzed during the three different rocket flights. The 15 January 2010 solar eclipse event and “SOUREX 1” wind and electron density measurements confirm the validity of the wind shear theory for equatorial regions during the eclipse and post sunset periods, when electrojet is weak, using wind and electron density irregularity measurements from the same instrument (ENWi) for the first time. The spectral indices in the range of −1.2 to −1.78 and the strong wind shear due to gravity wave winds during the eclipse time as well as the post sunset time, confirm the role of neutral turbulence in the generation of irregularities in the 95–112 km altitude region. The spectral index of −2.0 to −2.7 and the presence of irregularities in the negative gradient regions establishes the role of wind‐driven gradient drift instability (GDI) in generating irregularities during the SOUREX 1 post sunset flight for altitudes below 93 km. Further, the role of gradient drift instability in triggering ionization irregularities during the daytime on 14 January 2010 is unraveled by the spectral index of −2.03 and the presence of irregularities in the positive gradient regions alone.