The transport of secretory proteins from the endoplasmic reticulum (ER) to the Golgi depends on COPII-coated vesicles. While the basic principles of the COPII machinery have been identified, it remains largely unknown how COPII transport is regulated to accommodate tissue- or activation-specific differences in cargo load and identity. To address this question we have used T cells as a model system that show strongly increased secretory cargo load upon activation. We have confirmed increased ER-export efficiency in activated T cells and then used RNA-Seq to uncover the molecular mechanism for this adaptation. While we do not find substantial changes in the abundance of mRNAs encoding for components of the early secretory pathway, we observe a strong change in alternative splicing of Sec16, a protein essential for COPII vesicle generation. Using Morpholino-mediated manipulation of alternative splicing as well as CRISPR/Cas9-mediated genome engineering we show that this splicing switch controls the number of ER exit sites and transport efficiency. Our work provides the first connection between the COPII pathway and alternative splicing thus adding a new regulatory layer to protein secretion and its adaptation to changing cellular environments. As a mechanistic basis, we suggest the C-terminal Sec16 domain to be a splicing-controlled protein-interaction platform, with individual isoforms showing differential ability to recruit COPII components (Wilhelmi et al., 2016, Nat Comm). We are now generating isoform-specific Sec16 knock-out mice to correlate Sec16 alternative splicing with in vivo phenotypes. Based on this first example we are also analyzing a broader impact of alternative splicing in controlling the functionality of the early secretory pathway.