A number of recent reports suggest that the functional specialization of plant cells in storage organs can influence subcellular protein sorting, so that the fate of a recombinant protein tends to differ between seeds and leaves. In order to test the general applicability of this hypothesis, we investigated the fate of a model recombinant glycoprotein in the leaves and seeds of a leguminous plant, Medicago truncatula. Detailed analysis of immature seeds by immunofluorescence and electron microscopy showed that recombinant phytase carrying a signal peptide for entry into the endoplasmic reticulum was efficiently secreted from storage cotyledon cells. A second version of the protein carrying a C-terminal KDEL tag for retention in the endoplasmic reticulum was predominantly retained in the ER of seed cotyledon cells, but some of the protein was secreted to the apoplast and some was deposited in storage vacuoles. Importantly, the fate of the recombinant protein in the leaves was nearly identical to that in the seeds from the same plant. This shows that in M. truncatula, the unanticipated partial vacuolar delivery and secretion is not a special feature of seed cotyledon tissue, but are conserved in different specialized tissues. Further investigation revealed that the unexpected fate of the tagged variant of phytase likely resulted from partial loss of the KDEL tag in both leaves and seeds. Our results indicate that the previously observed aberrant deposition of recombinant proteins into storage organelles of seed tissue is not a general reflection of functional specialization, but also depends on the species of plant under investigation. This discovery will have an impact on the production of recombinant pharmaceutical proteins in plants.