Global Navigation Satellite Systems’ radio occultation (GNSS-RO) provides the upper troposphere-lower stratosphere (UTLS) vertical atmospheric profiles that are complementing radiosonde and reanalysis data. Such data are employed in the numerical weather prediction (NWP) models used to forecast global weather as well as in climate change studies. Typically, GNSS-RO operates by remotely sensing the bending angles of an occulting GNSS signal measured by larger low Earth orbit (LEO) satellites. However, these satellites are faced with complexities in their design and costs. CubeSats, on the other hand, are emerging small and cheap satellites; the low prices of building them and the advancements in their components make them favorable for the GNSS-RO. In order to be compatible with GNSS-RO requirements, the clocks of the onboard receivers that are estimated through the precise orbit determination (POD) should have short-term stabilities. This is essential to correctly time tag the excess phase observations used in the derivation of the GNSS-RO UTLS atmospheric profiles. In this study, the stabilities of estimated clocks of a set of CubeSats launched for GNSS-RO in the Spire Global constellation are rigorously analysed and evaluated in comparison to the ultra-stable oscillators (USOs) onboard the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC-2) satellites. Methods for improving their clock stabilities are proposed and tested. The results (i) show improvement of the estimated clocks at the level of several microseconds, which increases their short-term stabilities, (ii) indicate that the quality of the frequency oscillator plays a dominant role in CubeSats’ clock instabilities, and (iii) show that CubeSats’ derived UTLS (i.e., tropopause) atmospheric profiles are comparable to those of COSMIC-2 products and in situ radiosonde observations, which provided external validation products. Different comparisons confirm that CubeSats, even those with unstable onboard clocks, provide high-quality RO profiles, comparable to those of COSMIC-2. The proposed remedies in POD and the advancements of the COTS components, such as chip-scale atomic clocks and better onboard processing units, also present a brighter future for real-time applications that require precise orbits and stable clocks.