Ticks and associated tick-borne diseases in livestock remain a major threat to the health of animals and people worldwide. However, in the United Arab Emirates (UAE), very few studies have been conducted on tick-borne microorganisms thus far. The purpose of this cross-sectional DNA-based study was to assess the presence and prevalence of tick-borne Francisella sp., Rickettsia sp., and piroplasmids in ticks infesting livestock, and to estimate their infection rates. A total of 562 tick samples were collected from camels, cows, sheep, and goats in the Emirates of Abu Dhabi, Dubai, and Sharjah from 24 locations. DNA was extracted from ticks and PCR was conducted. We found that Hyalomma dromedarii ticks collected from camels had Francisella sp. (5.81%) and SFG Rickettsia (1.36%), which was 99% similar to Candidatus Rickettsia andeanae and uncultured Rickettsia sp. In addition, Hyalomma anatolicum ticks collected from cows were found to be positive for Theileria annulata (4.55%), whereas H. anatolicum collected from goats were positive for Theileria ovis (10%). The widespread abundance of Francisella of unknown pathogenicity and the presence of Rickettsia are a matter of concern. The discovery of T. ovis from relatively few samples from goats indicates the overall need for more surveillance. Increasing sampling efforts over a wider geographical range within the UAE could reveal the true extent of tick-borne diseases in livestock. Moreover, achieving successful tick-borne disease control requires more research and targeted studies evaluating the pathogenicity and infection rates of many microbial species.