Real-time monitoring of toxic gases and breath markers can be performed by metal oxide semiconductor-based chemo-resistive gas sensors due to their simple structures, low cost, and faster and better recovery and response. Due to the effective electron-hole separation, tuning the development of phase junctions of the metal oxide is an efficient method for improving their gas sensing properties. In this study, two distinct hydrothermal methods were used to synthesize h-/m-WO3 hetero-nanoflowers. In the first method, L-Cysteine was used to facilitate the formation of phase junctions between h-WO3 and m-WO3 nanostructures, whereas Thiourea was used in the second. Various characterisation approaches validated the hexagonal-monoclinic phase junction development in the nanoflowers. The sensing material fabricated using Thiourea with a concentration of 0.01M performed better than other sensors. At 350°C, the selected sample displayed outstanding ammonia sensing capacity with the experimental detection limit of 1 ppm (response=3.33). The theoretical detection limit is determined to be 27 ppb. The selectivity of the sensor towards NH3 over H2S and acetone is increased by combining the devices with a double filtration setup. The effectiveness of the selected h-/m-WO3 sensor for diagnosing kidney dysfunction was evaluated by analyzing simulated breath samples.