The inner walls of fused silica micro-capillaries were successfully coated with polyaniline nanofibres using the “grafting” approach. The optical response of polyaniline coatings was evaluated during the subsequent redoping–dedoping processes with hydrochloric acid and ammonia solutions, respectively, that were passed inside the micro-capillary in continuous flow. The optical absorbance of the polyaniline coatings was measured and analysed in the wavelength interval of [300–850 nm] to determine its optical sensitivity to different concentrations of ammonia. It was found that the optical properties of polyaniline coatings change in response toammonia solutions in a wide concentration range from 0.2 ppm to 2000 ppm. The polyaniline coatings employed as a sensing material for the optical detection of aqueous ammonia have a fast response time and a fast regeneration time of less than 5 seconds at room temperature. The coating was fully characterised by Scanning Electron Microscopy, Raman Spectroscopy, absorbance measurements and kinetic studies. The response of the coatings showed very good reproducibility, demonstrating that this platform can be used for the development of micro-capillary integrated sensors based on the inherited sensing properties of polyaniline.