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Molecular diagnostic tests are widely implemented in animal and human health microbiology. Efficient nucleic acid extraction methods are essential in diagnostic laboratories and automation is a valuable tool for those with high throughput activity. Nucleic acid extraction protocols present variable efficiency depending on the composition of the specimen and the chemical-physical characteristics of the target pathogen. In the present study, we compared the DNA extraction performances of four automated methods (kits I, M, P, Q) adapted on a Hamilton Robotics “Microlab Starlet” extraction unit, and one manual method (kit R). Ten-fold dilutions of Mycobacterium avium subsp. paratuberculosis (MAP) were used to contaminate bovine central nervous system (CNS) and lung-spleen-liver pools (LSL). In consideration of its chemical-physical characteristics, MAP was selected as a template for pathogen DNA detection. Analytical performance and repeatability were assessed through downstream real-time PCR amplification, hands-on time (HOT), total turnaround time (TAT) and costs of all kits. MAP was detected differently depending on extraction kit and type of matrix analysed. Kits M and I showed the highest analytical performance on CNS (1 MAP/ml) and LSL (10 MAP/ml), respectively. Besides analytical results, kits I and M displayed high repeatability, the same HOT, very similar TAT, and were inexpensive. In conclusions, different standardized automated systems have been established with high throughput, sensitivity and repeatability for CNS and LSL. Our results also demonstrated that is necessary to assess the effectiveness of extraction kits in matrices not previously tested to avoid the risk of unreliable diagnostic outcomes.