The success of bioanalytical technologies deployed at decentralised settings is governed by various performance criteria such as user-friendliness, ease-of-use, cost per-test (at comparatively low sample throughput) and adaptability to a wide range of available analytes while performing with minimal instrumentation. The centrifugal microfluidic “Lab-on-a-Disc” (LoaD) platform is a highly customisable platform which can meet these criteria for decentralised testing. However, a key concern of LoaD systems is the difficulty in implementing reliable flow routing and valving on a rapidly rotating cartridge. To address this challenge, we demonstrate here, the microfluidic automation of a bead-based Enzyme-Linked Immuno-Sorbent Assays (ELISAs) through use of a novel solvent-selective membrane and centrifugal-stratification enabled router architecture. To rule out optical interference of the bead phase with the absorption measurements, we use these novel lipophilic membrane valves to route the reaction product of the ELISA from the bead-phase into a separate detection chamber. As a pilot application, we automate a Rapid Antigenic Protein in situ Display (RAPID) ELISA for detection of the E7 antibody biomarker, which is clinically relevant for HPV16 virus related cervical cancer, on a LoaD cartridge. Through combination of this membrane and routing technology with event-triggered valves, the assay is implemented in an entirely automated fashion using minimal instrumentation (low-cost spindle motor). Furthermore, our approach is highly flexible as the RAPID protocol can be customised to a specific target by functionalising the bead-based solid-phase with specific proteins.