A selective molecularly imprinted polymer (MIP) adsorbent was synthesised and used in a batch micro-solid phase extraction format for isolating aflatoxins (AFB1, and AFB2) from non-dairy beverages before liquid chromatography-tandem mass spectrometry determination. MIP synthesis (precipitation polymerization in 3 : 1 acetonitrile/toluene as a porogen) was performed with 5,7-dimethoxycoumarin (DMC), methacrylic acid (MAA) and divinylbenzene-80 (DVB) as a dummy template, functional monomer and cross-linker, respectively (1 : 4 : 20 molar ratio). 2,2′-Azobisisobutyronitrile (AIBN) was used as a polymerization initiator. The adsorbent MIP (50 mg) was enclosed in a cone-shaped polypropylene membrane (porous membrane protected molecularly imprinted micro-solid phase extraction), and parameters such as sample pH, mechanical (orbital-horizontal) shaking, the extraction time (loading stage), the composition of the eluting solution, and the desorption time were optimised. The highest extraction yields were obtained by using 5 mL of non-dairy beverages (pH adjusted at 6.0), and mechanical shaking (150 rpm) for 15 min. Elution was performed with 5 mL of an acetonitrile/formic acid (97.5 : 2.5) mixture under ultrasound (325 W, 35 kHz) for 15 min. After eluate evaporation to dryness and re-dissolution in 150 μL of the mobile phase, the pre-concentration factor of the method was 33.3, which yields limits of detection within the 0.085–0.207 μg L⁻¹ range. In addition, the current proposal was shown to be an accurate and precise method through relative standard deviation of intraday and inter-day assays below 18% and analytical recoveries in the range of 91–104%. However, the method was found to suffer from matrix effects.