The microsomal epoxide hydrolase (mEH) is important in the detoxification of carcinogens in the liver and other tissues but is also a blood biomarker of hepatitis and liver cancer. Improved analytical methods are needed for the study of its role in the metabolism of xenobiotics and endogenous roles as a blood biomarker of diseases. The development of a double nanobody sandwich ELISA offers significant improvements over traditional polyclonal or monoclonal antibody-based assays, enhancing both the homogeneity and the stability of assay production. This study focuses on selecting and optimizing nanobody pairs for detecting human mEH. Four high-affinity nanobodies were identified and tested for thermal stability. Combinations of these nanobodies were evaluated, revealing that the MQ4-MQ30 pair achieved the best performance with a limit of detection (LOD) of 1 ng/mL. Additionally, polyHRP was also employed for signal amplification, enhancing detection capabilities despite challenges related to the small size and single epitope recognition of the nanobodies. Comparative studies using microplates and NHS@MF membranes were also performed. The superior performance of the NHS@MF membranes highlighted their potential as a promising alternative for point-of-care testing. The assay exhibited high specificity for human mEH and minimal cross-reactivity with related enzymes and effectively addressed matrix effects in plasma and tissue samples. These findings underscore the potential of double nanobody sandwich ELISAs for reliable and sensitive biomarker detection.