Concentrations of ammonia in biological processes were controlled by PID controllers and also neural network based controllers (NN controllers). A flow injection analysis system has been to on-line monitor the concentrations of ammonia in a bioreactor. The effect of the analysis error and the residence time of samples on the control performance were studied. The optimal neural network structure was investigated by using computer simulation and found to be a 3(input layer)-2(hidden layer)-1(output layer). The NN controller is often time consuming, but it has advantage over the PID controller in sensitivity. The 3-2-1 NN controller has been applied to control the ammonia concentrations in a simulated bioprocess and also a real cultivation process of yeast. The good control performance showed that the 3-2-1 NN controller based on the FIA system can be used to control the concentration of substrates in biological processes very well.