A novel, miniaturized microfluidic platform was developed for the simultaneous detection and removal of polybrominated diphenyl ethers (PBDEs). The platform consists of a polydimethylsiloxane (PDMS) microfluidic chip for an immunoreaction step, a PDMS chip with an integrated screen-printed electrode (SPCE) for detection, and a PDMS-reduced graphene oxide (rGO) chip for physical adsorption and subsequent removal of PBDE residues. The detection was based on competitive immunoassay-linked binding between PBDE and PBDE modified with horseradish peroxidase (HRP-PBDE) followed by the monitoring of enzymatic oxidation of o-aminophenol (o-AP) using square wave anodic stripping voltammetry (SW-ASV). PBDE was detected with good sensitivity and a limit of detection similar to that obtained with a commercial colorimetric test (0.018 ppb), but with the advantage of using lower reagent volumes and a reduced analysis time. The use of microfluidic chips also provides improved linearity and a better reproducibility in comparison to those obtained with batch-based measurements using screen-printed electrodes. In order to design a detection system suitable for toxic compounds such as PBDEs, a reduced graphene oxide–PDMS composite was developed and optimized to obtain increased adsorption (based on both the hydrophobicity and π–π stacking between rGO and PBDE molecules) compared to those of non-modified PDMS. To the best of our knowledge, this is the first demonstration of electrochemical detection of flame retardants and a novel application of the rGO-PDMS composite in a biosensing system. This system can be easily applied to detect any analyte using the appropriate immunoassay and it supports operation in complex matrices such as seawater.