Q fever represents an important 'neglected zoonosis', with high prevalences recorded across the Middle East region. Among rural desert-dwelling communities in the region, camel milk is largely consumed raw, due to perceptions of dromedaries as a uniquely clean livestock species mentioned in the Qur'an and Islamic hadith, while milk from other livestock species is usually boiled. As a result, camels present a unique public health threat among such communities from milk-borne pathogens, including Coxiella burnetii. In view of this, a cross-sectional study was conducted among dromedary herds in southern Jordan between September 2017 and October 2018, including 404 camels from 121 randomly selected herds. In addition, 510 household members associated with these herds were interviewed regarding potential high-risk practices for zoonotic transmission. Weight adjusted camel population seroprevalence for C. burnetii was 49.6% (95% CI: 44.7-54.5), with evidence of maternally derived immunity in calves ≤6 months old. Adjusted herd-level prevalence was 76.0% (95% CI 72.7-80.2). It was estimated 30.4% (144/477) of individuals consumed raw milk from infected herds monthly or more. Following multivariable logistic regression analysis, seropositive status in camels was found to be associated with increasing age, high herd tick burdens, keeping the herd together throughout the year including when calving, and owning larger (>50) sheep and goat flocks, with goats presenting a higher risk than sheep. Racing camel status was found to be protective. Socioculturally appropriate interventions aimed at raising awareness of potential risks associated with drinking raw camel milk, alongside appropriate livestock management interventions, should be considered.