Metabolic substances play a pivotal role in maintaining the body’s regular physiological functions. When these processes are disrupted, it can lead to metabolic disorders which have the potential to cause severe damage to various organs. Diabetes mellitus, a prevalent metabolic disorder, arises from disturbances in sugar metabolism among other substances. Consequently, there’s a pressing need to monitor metabolite levels for early diagnosis. To address this, our study introduces a semi‐implantable metabolite sensing system developed around functionalized microwires‐based bundle electrodes (FMBE). This FMBE device offers real‐time, sensitive, and continuous tracking of glucose, hydrogen peroxide (H2O2), and uric acid (UA) levels in the body, allowing an in‐depth assessment of subcutaneous metabolite concentrations. The FMBE was coated with Au nanoclusters and CNT‐MXene nanocomposites to enhance sensing surface area. In vitro characterizations affirmed the FMBE’s linear responsivity, detection sensitivity, and selectivity towards glucose, H2O2, and UA sensing. In addition, in vivo testing in healthy and diabetic rats demonstrated that FMBE was able to continuously monitor interstitial glucose, H2O2, and UA concentrations after implantation. The FMBE system, thus, stands out as a promising platform for real‐time, in‐situ monitoring of metabolite concentrations, potentially assisting in the diagnosis of diabetes and associated complications.This article is protected by copyright. All rights reserved.