Pichia pastoris is a cheaper alternative to CHO for the expression of glycosylated proteins. A method has been developed and implemented in Pichia for large scale, economical purification of recombinant proteins. This method utilizes self-cleaving inteins to link purification tags and target proteins, thereby eliminating the need for proteolytic tag removal and making the method economically feasible on larger scales. Both chromatographic and non-chromatographic purification tags were investigated in shake flask and fermentation cultures. A chitin-binding domain tag was successfully used to purify various proteins on chitin affinity resin. In addition, a non-chromatographic elastin-like polypeptide (ELP) purification tag was investigated. In the latter purification scheme, mild temperature shifts induce ELP aggregation and dissociation. This reversible precipitation allows for the separation of the ELP-bound target protein using a series of temperature shifts and centrifugation, ultimately resulting in a simple, economical purification system.