Understanding the cellular responses caused by metabolic stress is crucial for the design of robust fed‐batch bioprocesses that maximize the expression of recombinant proteins. Chinese hamster ovary cells were investigated in chemically defined, serum‐free cultures yielding 107 cells/mL and up to 500 mg/L recombinant tissue‐plasminogen activator (t‐PA). Upon glutamine depletion increased autophagosome formation and autophagic flux were observed, along with decreased proliferation and high viability. Higher lysosomal levels correlated with decreased productivity. Chemical inhibition of autophagy with 3‐methyl adenine (3‐MA) increased the t‐PA yield by 2.8‐fold. Autophagy‐related MAP1LC3 and LAMP2 mRNA levels increased continuously in all cultures. Analysis of protein quality revealed that 3‐MA treatment did not alter glycan antennarity while increasing fucosylation, galactosylation, and sialylation. Taken together, these findings indicate that inhibition of autophagy can considerably increase the yield of biotechnology fed‐batch processes, without compromising the glycosylation capacity of cells. Monitoring or genetic engineering of autophagy provides novel avenues to improve the performance of cell culture‐based recombinant protein production. Biotechnol. Bioeng. 2012; 109:1228–1238. © 2011 Wiley Periodicals, Inc.