Novel flexible NH3 gas sensors were formed by the in situ self-assembly of polypyrrole (PPy) on plastic substrates. A negatively charged substrate was prepared by the formation of an organic monolayer (3-mercapto-1-propanesulfonic acid sodium salt—MPS) on a polyester (PET) substrate using a pair of comb-like Au electrodes. Two-cycle poly(4-styrenesulfonic acid) sodium salt/poly(allylamine hydrochloride) (PSS/PAH) bilayers (precursor layer) were then layer-by-layer (LBL) deposited on an MPS-modified substrate. Finally, a monolayer of PPy self-assembled in situ and PPy multilayer thin films self-assembled LBL in situ on a (PSS/PAH)2/MPS/Au/Cr/PET substrate. The thin films were analyzed by atomic force microscopy (AFM). The effects of the precursor layer (PSS), the deposition time of the monolayer of PPy and the number of PPy multilayers on the gas sensing properties (response) and the flexibility of the sensors were investigated to optimize the fabrication of the film. Additionally, other sensing properties such as sensing linearity, reproducibility, response and recovery times, as well as cross-sensitivity effects were studied. The flexible NH3 gas sensor exhibited a strong response that was comparable to or even greater than that of sensors that were fabricated on rigid substrate at room temperature.