There exists a strong correlation between the pH levels of the gastrointestinal (GI) tract and GI diseases such as inflammatory bowel disease (IBS), ulcerative colitis, and pancreatis. Existing methods for diagnosing many GI diseases predominantly rely on invasive, expensive, and time-consuming techniques such as colonoscopy and endoscopy. In this study, an autonomous ingestible smart biosensing system in a pill format with integrated pH sensors is reported. The smart sensing pills will measure the pH profile as they transit through the GI tract. The data is then downloaded from the pills after they are collected from the feces. The sensor is based on electrodeposited PANI on carbon-coated conductive threads providing high pH sensitivity. Engineering innovations allowed integration of thread-based sensors on 3D-printed pill surfaces with front-end readout electronics, memory, and microcontroller assembled on mm-size circular printed circuit boards. The entire smart sensing pill possesses an overall length of 22.1 mm and an outer diameter of 9 mm. The modular biosensing system allows integration of thread-based biosensors to monitor other biomarkers in GI tract that mitigates the complex sensor fabrication process as well as overall pill assembly.