One of the frontier research areas in the field of gas sensing is high-performance room temperature-based novel sensing materials, and new family of low-cost and eco-friendly carbon nanomaterials with a unique structure has attracted significant attention. In this work, we propose a novel low-cost flexible room temperature ammonia gas sensor based on nitrogen-doped carbon nano-onions/polypyrrole (NCNO-PPy) composite material mounted low-cost membrane substrate was synthesized by combining hydrothermal and in-situ chemical polymerization methods. The proposed flexible sensor revealed high sensing performance when employed as the sensing material for ammonia detection at room temperature. The NCNO-PPy ammonia sensor exhibited 17.32% response for 100 ppm ammonia concentration with a low response time of 26 s. The NCNO-PPy based flexible sensor displays high selectivity, good repeatability, and long-term durability with 1 ppm as the lower detection limit. The proposed flexible sensor also demonstrated remarkable mechanical robustness under extreme bending conditions, i.e., up to 90° bending angle and 500 bending cycles. This enhanced sensing performance can be related to the potential bonding and synergistic interaction between nitrogen-doped CNOs and PPy, the formation of defects from nitrogen doping, and the presence of high reactive sites on the surface of NCNO-PPy composites. Additionally, the computational study was performed on optimized NCNO-PPy nanocomposite for both with and without NH3 interaction. A deeper understanding of the sensing phenomena was proposed by the computation of several electronic characteristics, such as band gap, electron affinity, and ionization potential, for the optimized composite.