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Monitoring wildlife populations at scale is fraught with logistical and resource constraints. Despite this, estimating wildlife population state variables and vital rates remains crucial for science, and to assess conservation investment and effort. The veracity and transparency of results also helps prevent politicization of wildlife populations. In Uganda, robust estimates of carnivore population size are rare in the literature. To overcome a near two-decade long data gap we initiated a survey of African lions, leopards, and spotted hyenas with the Uganda Wildlife Authority across six important protected areas. Surveys were conducted within a spatial capture-recapture framework, the industry gold-standard for monitoring carnivore populations. For lions, we used unstructured spatial sampling protocols (in the form of vehicle-based searches), while for leopards, and spotted hyenas we deployed camera traps. Our protocols were designed to obtain unambiguous individual identification photographs. This large-scale effort involved data collection by >100 local conservation stakeholders (including lodge guides, trophy hunters, university students, and government rangers). Locally extinct in three areas, we show lion numbers are precariously low in two of three sites where they still occur (Queen Elizabeth abundance=39.72, Posterior standard deviation (PSD)=7.96; Kidepo Valley abundance=22.23, PSD=11.67). Murchison Falls was identified as Uganda’s lion stronghold with an estimate of ∼240 individuals (PSD=34) and average park-wide densities of 7.43 individuals/100 km2 (PSD=1.05). Leopard densities were highest in Lake Mburo and Murchison Falls. In Murchison they reach some of the highest densities in Africa (14.06 individuals/100 km2, PSD=2.65). Spotted hyena densities were high compared to lions (range=6.15–45.31 individuals/100 km2), except in Lake Mburo where densities were markedly lower (park abundance=23 individuals in 370 km2, PSD=5.26). Our work has critical policy implications, and forms the foundation of the new Strategic Action Plan for Large Carnivore Conservation in Uganda (2023–2033). It also illustrates how cutting-edge, transparent and collaborative science, implemented by multiple wildlife conservation stakeholders can help gauge the conservation status of their wildlife resources.