Insufficient accumulation and the lack of efficient purification methods are the two major bottlenecks hindering the recombinant production of many proteins. Alternative production schemes are urgently needed for proteins that remain challenging to express and purify with conventional techniques. We have found that hydrophobin fusions targeted to endoplasmic reticulum (ER) can enhance the expression of target proteins simultaneously providing means for straightforward purification. Here we show that hydrophobin fusion technology induces formation of large protein bodies in the filamentous fungus Trichoderma reesei. The fusion protein remained soluble in the ER-derived protein bodies. A simple and scalable aqueous two-phase system was demonstrated to purify the hydrophobin fusion protein GFP-HFBI from the complex intracellular extracts with a recovery of up to 62%.