In the life sciences, automation solutions are primarily established in the field of drug discovery. However, there is also an increasing need for automated solutions in the field of medical diagnostics, e.g., for the determination of vitamins, medication or drug abuse. While the actual metrological determination is highly automated today, the necessary sample preparation processes are still mainly carried out manually. In the laboratory, flexible solutions are required that can be used to determine different target substances in different matrices. A suitable system based on an automated liquid handler was implemented. It has been tested and validated for the determination of three cannabinoid metabolites in blood, urine and saliva. To extract Δ9-tetrahydrocannabinol-D3 (Δ9-THC-D3), 11-hydroxy-Δ9-tetrahydrocannabinol (THC-OH) and 11-nor-9-carboxy-Δ9-tetrahydrocannabinol (THC-COOH) from serum, urine and saliva both rapidly and cost-effectively, three sample preparation methods automated with a liquid handling robot are presented in this article, the basic framework of which is an identical SPE method so that they can be quickly exchanged against each other when the matrix is changed. If necessary, the three matrices could also be prepared in parallel. For the sensitive detection of analytes, protein precipitation is used when preparing serum before SPE and basic hydrolysis is used for urine to cleave the glucuronide conjugate. Recoveries of developed methods are >77%. Coefficients of variation are <4%. LODs are below 1 ng/mL and a comparison with the manual process shows a significant cost reduction.