For the first time, the effect of electroendosmosis (EEO) flow phenomenon was investigated in detail, on the gel electromembrane extraction (G-EME). When electric field is used as an actuator of ion transport in G-EME, the EEO flow phenomenon can occur within the agarose gel membrane interface and is generally considered the dominant issue. In this regard, various agarose-based gel membrane types with low-, medium- and high-EEO were fabricated and tested. To further diminish the EEO effect, the different gel membrane additives such as dextrin, chitosan and xylan with different concentrations i.e., 5%, 10% and 15% were also examined. The positively charged Cr(III) and negatively charged Cr(VI) were chosen as model analytes. The Cr(III) and Cr(VI) were simultaneously extracted from an aqueous sample (pH 3.0) via the cathodic and anodic gel membranes (pH 3.0 for both membranes), into the cathodic and anodic aqueous acceptors (200 µL each, pH 2.0), respectively. After extraction at the optimal conditions (i.e., voltage: 32 V, extraction time: 22 min), the both compounds were quantified by a cheap and easy-to-perform reader platform termed as microfluidic paper-based analytical device (μPAD). The results showed that high extraction recoveries such as 87% for Cr(III) and 75% for Cr(VI), were acquired when the low-EEO agarose gel membrane with 5% (w/v) dextrin was used. On the other hand, using the high-EEO agarose gel membrane with no additive lead to the high EEO flow and the increase of cathodic acceptor volume (equal to 350 µL) while the recovery depressed to about 50% due to the dilution effect. Simultaneously, the volume of anodic acceptor became almost vacant (~50 µL). Ultimately, by means of such simple gel membrane adjusting (i.e., low-EEO agarose with 5% dextrin), the both target compounds were quantitatively extracted at a single step achieving limits of detection (LODs) of 0.5 and 0.7 ng mL−1 for Cr(III) and Cr(VI), respectively.