A wide range of plant species, including economically important crops such as vegetables, ornamentals, bulbs, and fundamentally fruits, can be affected by gray mold caused by the fungal pathogen Botrytis cinerea . This paper describes the development of a microfluidic immunosensor with micromagnetic beads (MMBs) coupled to carbon-based screen-printed electrodes (SPCEs) for the rapid and sensitive quantification of B. cinerea in apple (Red Delicious), table grape (pink Moscatel), and pear (William's) tissues. The detection of B. cinerea was carried out using a competitive immunoassay method based on the use of purified B. cinerea antigens immobilized on 3-aminopropyl-modified MMBs. The total assay time was 40 min, and the calculated detection limit was 0.008 μg mL(-1). Moreover, the intra- and interassay coefficients of variation were below 7%. The developed method allowed detects B. cinerea even in asymptomatic fruits and promises to be particularly useful for application in the agricultural industry.