In-vitro physiologically relevant gastrointestinal extraction based on the validated Unified BARGE Method (UBM) is in this work hyphenated to inductively coupled plasma optical emission spectrometry in a batch-flow configuration for real-time monitoring of oral bioaccessibility assays with high temporal resolution. A fully automated flow analyzer is designed to foster in-line filtration of gastrointestinal extracts at predefined times (≤15 min) followed by on-line multi-elemental analysis of bioaccessible micro-nutrients, viz., Cu, Fe and Mn, in well-defined volumes of extracts (300 µL) of transgenic and non-transgenic soybean seeds taken as model samples. The hyphenated flow setup allows for recording of temporal extraction profiles to gain full knowledge of the kinetics of the gastrointestinal digestion processes, including element leaching and concomitant precipitation and complexation reactions hindering bioavailability. Simplification of the overall standard procedure is also feasible by identification of steady-state extraction conditions. Our findings indicate that reliable measurement of oral bioaccessible pools of Cu, Fe and Mn in soybean might be obtained in less than 180 min rather than 240 min as endorsed by UBM. Using a matrix-matched external calibration, limits of detection according to the 3s criteria were 0.5 µg/g for Mn, 0.6 µg/g for Cu and 2.3 µg/g for Fe. Trueness of the automatic bioaccessibility method was confirmed by mass balance validation with recoveries ranging from 87 to 116% regardless of the target element and sample. Cu was the micronutrient with the highest oral bioaccessibility ranging from 73% to 83% (7.5-7.9 µg/g) for non-transgenic and transgenic soybeans, respectively, followed by Mn and Fe within the ranges of 29-31% (10.8-11.4 µg/g) and 11-15% (8-14 µg/g), respectively, regardless of transgenesis. The proposed kinetic method is proven suitable for fast and expedient estimation of the nutritional value of soybeans and elucidation of the potential effect of transgenesis onto bioaccessible fractions of elements.