Particle number densities are a crucial parameter in the microstructure engineering of microalloyed steels. We introduce a new method to determine nanoscale precipitate number densities of macroscopic samples that is based on the matrix dissolution technique (MDT) and combine it with atom probe tomography (APT). APT counts precipitates in microscopic samples of niobium and niobium-titanium microalloyed steels. The new method uses MDT combined with analytical ultracentrifugation (AUC) of extracted precipitates, inductively coupled plasma–optical emission spectrometry, and APT. We compare the precipitate number density ranges from APT of 137.81 to 193.56 × 1021 m−3 for the niobium steel and 104.90 to 129.62 × 1021 m−3 for the niobium-titanium steel to the values from MDT of 2.08 × 1021 m−3 and 2.48 × 1021 m−3. We find that systematic errors due to undesired particle loss during extraction and statistical uncertainties due to the small APT volumes explain the differences. The size ranges of precipitates that can be detected via APT and AUC are investigated by comparison of the obtained precipitate size distributions with transmission electron microscopy analyses of carbon extraction replicas. The methods provide overlapping resulting ranges. MDT probes very large numbers of small particles but is limited by errors due to particle etching, while APT can detect particles with diameters below 10 nm but is limited by small-number statistics. The combination of APT and MDT provides comprehensive data which allows for an improved understanding of the interrelation between thermo-mechanical controlled processing parameters, precipitate number densities, and resulting mechanical-technological material properties.