Animals are expected to engage in behavioral decision-making that minimizes their risk of predation; these decisions can cause non-lethal predator effects to behavior and spatial use. Our goal was to determine whether non-lethal effects of a common predator, coyotes (Canis latrans), could affect the behavior of a declining reptile, the Mojave Desert tortoise (Gopherus agassizii), hereafter tortoise. We exposed captive tortoises to olfactory and visual cues of coyotes and measured their resulting foraging behavior, burrow use, and other antipredator behaviors. We also measured risk of coyote predation in wild tortoises based on burrow use. Willingness to feed and time spent feeding were unaffected by the presence of coyote urine, but higher air temperatures at the start of feeding caused a decrease in time spent at their food dish. Captive tortoises chronically exposed to coyote urine did, however, spend more time in their burrows than when exposed to rabbit urine. When exposed to a coyote decoy, captive tortoises showed more general antipredator behaviors than those exposed to a control stimulus (deer decoy). Wild tortoises were less likely to be depredated by coyotes, if they were encountered in burrows more frequently. Predator olfactory and visual cues exerted non-lethal effects on captive tortoises through behavioral adjustments to their refuge-seeking behavior, which was a behavior linked to decreased coyote predation risk for wild tortoises. Human-subsidized predator populations may negatively affect declining species, including reptiles, as a result of behavioral modifications in response to predator cues. Predators can affect behavior of animals through olfactory and visual cues, which can have measurable effects on prey populations. Changes in prey behavior in response to predator presence can occur at the expense of opportunities to forage or reproduce, leading to decreased survival and reproduction. We tested behavioral responses of captive Mojave Desert tortoises to olfactory and visual cues of coyotes, which are a common predator in the Mojave Desert and subsidized by human food sources. Foraging behavior of captive tortoises was strongly affected by air temperatures at the start of feeding, but not coyote cues. Captive tortoises did, however, increase the amount of time they spent in burrows when coyote urine was present and showed greater fearfulness at the presentation of coyote urine combined with coyote models. Increased burrow use was associated with lower risk of coyote predation in wild tortoises, which suggested an advantage to increased refuge use when coyotes were detectable. Responses by tortoises suggest that coyote cues on the landscape affect tortoises through behavioral pathways that result in increased refuge use.