Surface plasmon resonance (SPR) currently is the major platform to study protein–protein interactions, but it lacks the selectivity to distinguish between binding components within one sample. Capillary electrophoresis (CE) can provide efficient separation of intact proteins under near-physiological conditions. We have hyphenated CE with SPR to achieve affinity assessment of mixture components. A microfluidic flow cell allowing straightforward coupling of CE and SPR was developed. Initial testing with non-interacting dyes showed good performance using a flow-cell channel volume of 100nL until the detection point. Appropriate closing of the CE electric circuit was achieved using the SPR gold-sensor as grounding electrode. Division of the (bio)sensor into an electrode part (providing grounding) and a detection part (bearing the affinity surface) was crucial to avoid disturbance of the SPR signal by the CE voltage. This approach permitted CE separation and binding assessment for separation voltages up to 30kV. Human serum albumin (HSA) or aprotinin were immobilized on carboxymethyldextran hydrogel-coated gold sensors and target proteins (anti-HSA, and trypsin and α-chymotrypsin, respectively) were analyzed. Efficient CE separation of the intact protein analytes was accomplished under native conditions by employing neutral and positively-charged capillary coatings. Selective binding of separated proteins to the target surface could be monitored by SPR down to 2ng of injected protein. Regeneration of the biosensor surface was achieved by an on-line rising, allowing repeatable CE-SPR analyses of proteins with RSDs below 1% and 5% for migration time and signal intensity, respectively.