The exposure of dairy cows to Coxiella burnetii using molecular and serological techniques was investigated in this study. Bulk tank milk and serum samples were collected from various farms in Greece (mainly northern Greece). DNA extraction was performed on milk samples, and qPCR targeting the IS1111 insertion sequence was performed to detect bacterial pathogens. An ELISA was used to detect specific antibodies in bulk milk and individual serum samples. Data on farms were collected in the field using handheld Global Positioning System Garmin units. The collected data were analyzed using an Ecological Niche Model within the framework of a geographic information system. The results indicated that in more than half of the dairy farms (35/60, 58.3%), C. burnetii is present in milk. Specific antibodies were also detected in almost all milk samples (57/60, 95.0%). At least one seropositive animal was identified using ELISA in the majority of the examined farms (25/28, 89.3%). C. burnetii PCR-positive farms were located in the low-altitude zone with a mean value of 97 m above sea level (range: 2–681). The environmental variable with the highest gain when used in isolation is precipitation in the wettest quarter (28.3% contribution), which therefore appears to have the most useful information by itself. The environmental variable that decreases the gain the most when omitted is the minimal temperature of the coldest month (6.9% contribution). The analysis demonstrated that a mild climate with low precipitation favors a positive status. The exposure of dairy cattle farms to C. burnetii is massive, raising significant concerns regarding livestock production and public health implications.