Transistor-based biochemical sensors are promising for biomarker detection, offering local signal amplification and compact form factors for miniaturized systems. However, many of these devices are optimized for single-analyte readout, and multiplexed sensing often increases system complexity. Moreover, these platforms rely on relatively rigid substrates, limiting conformal integration with soft biological tissues. Here, we present an ultrathin, multi-gate organic electrochemical transistor (OECT) and demonstrate a proof-of-concept, insertable-format platform for multiplexed biomarker sensing. The device was fabricated on a 4-μm-thick ultrathin parylene substrate and incorporates two gold gate electrodes independently functionalized with distinct aptamers, enabling two-analyte multiplexing on a single OECT channel. Each aptamer showed selective recognition of its target biomarker, and target binding was transduced at the gate and amplified as a measurable modulation of the OECT channel current. We integrated the device into a pill-shaped structure and demonstrated its functionality through ex vivo experiments in a porcine small intestine.