Effective expression of porcine interferon-alpha (pIFN-alpha) with recombinant Pichia pastoris was conducted in a bench-scale fermentor using an in situ methanol electrode-based feeding process with the control level of methanol concentration linearly increased to 10 g l(-1) for the first 20 h and maintained at 10 g l(-1) for the rest of expression phase. With this two-stage control process, the highest pIFN-alpha concentration reached a level of 1.81 g l(-1), which was 1.5-fold of that in the previous constant 10 g l(-1) induction experiments. There is an improvement of the pIFN-alpha productivity from more distribution of carbon flux to protein expression. The pIFN-alpha expression stability could be further enhanced by a simple on-line fault diagnosis method for methanol overfeeding based on oxygen uptake rate changing patterns. By implementing corrective action of feeding glycerol after fault detection, the production yield increased to twice the amount it would have been without the diagnosis.