This study investigates the performance of hydrophobic membrane contactors (HMC) for the recovery of dissolved ammonia (NH3) from natural rubber processing (NRP) wastewater during short- and long-term operation. The results show that 90% recovery of total NH3 nitrogen can be achieved. In the short-term operations, the increases in the wastewater velocity and pH enhanced the NH3 desorption overall mass transfer coefficient (KOV), but the increase in the number of total solids in the wastewater reduced the KOV. The Wilson plot method confirmed the significance of the mass transfer resistance of the wastewater phase for NH3 desorption. The long-term operation revealed that the KOV was kept constant for 15 days and then declined owing to membrane fouling. Flushing using water (physical cleaning) could not restore the KOV to its initial value, but a series of chemical cleanings with 0.1M NaOH and 0.1M HCl solution successfully recovered the KOV. The comparison of cleaning solutions in the foulant extraction’s ability showed that 0.1M NaOH was the most potent, followed by 0.1M HCl and water. Fouling characterization using scanning electron microscopy and energy dispersive X-ray spectrometry (SEM/EDS) and the Fourier transform infrared spectroscopy revealed a cake layer covering the membrane surface, and the foulants consisted of organic compounds composed of proteins from natural rubber (NR) particles and inorganic salts. The hydrophobic interaction of the proteins covering the NR particles allowed the natural rubber particles to be deposited on the membrane surface, even without hydraulic pressure in HMC. The negative charge of the NR particles could also interact with ions, leading to the formation of inorganic components in the fouling cake layers. Two types of fouled membrane surfaces were identified via SEM/EDS: a smooth area, which consisted of N-atom from proteins, and a rugged area with small conglomerate particles in which no N-atoms were observed.