Measurement of the dense cold thermal plasma in planetary ionospheres via orbiting spacecraft is challenging because ion energies are small (0–4 eV), densities can vary by four orders of magnitude, composition varies with altitude, spacecraft charging varies in time and must be measured very accurately, and instrumental effects (e.g., detector dead‐time and background) can be significant. The SupraThermal And Thermal Ion Composition instrument team has recently released a new set of data products that contain density moments of the primary ion species at Mars, including those derived at periapsis, subject to the full suite of calibration factors required. This article discusses the challenges associated with deriving these densities and provides examples of the key caveats that users of the data should be aware of. A preliminary statistical study of this new data set focuses on the structure and variability of Mars' ionosphere, demonstrating that solar zenith angle effects, the crustal magnetic fields, and electron precipitation on the nightside, drive the strongest structural features, consistent with photochemical theory and previous studies. Dayside ionospheric density profiles are highly repeatable below altitudes of 200 km, marking the region where photochemistry and collisions dominate. In the upper dayside ionosphere (altitudes >300–400 km) changes in the solar wind dynamic pressure on timescales of Mars Atmosphere and Volatile EvolutioN's orbit (hr) drive the largest (factors of 1–3) variability in ionospheric density. In contrast variability in ionospheric density peaks between 150 and 250 km altitude on the nightside (factors of 1–2), consistent with electron precipitation driving ionization in this region. Plain Language Summary Making accurate measurements of the ions present in planetary atmospheres via orbiting spacecraft is difficult due to the large changes in conditions encountered throughout spacecraft orbits. This paper describes the techniques implemented to address the full array of difficulties associated with measuring planetary ions at Mars using measurements made by the SupraThermal And Thermal Ion Composition instrument. These techniques are used to calculate ion densities in Mars' atmosphere and we perform a preliminary investigation of this new data set, revealing several important characteristics of how ions behave in Mars' atmosphere. In particular, we find that on the dayside of the planet, there is a transition region between the upper and lower atmosphere where planetary ions behave differently. Above this transition region planetary ions are influenced by forces that arise in the space environment about Mars, while below this transition region, planetary ions are well shielded from these effects. Our results provide insight into the processes that shape Mars' atmosphere and tell us how energy is transported through the Mars system. Key Points The calibration challenges and caveats of ion densities derived from SupraThermal And Thermal Ion Composition observations are discussed Solar zenith angle effects and the crustal magnetic fields drive the strongest structural features in ionospheric density A variety of processes drive ionospheric variability throughout different regions of the Martian ionosphere