Determination of material properties and functions is a crucial step towards optimization of fabrication methods as well as the development of electrospun nanofibers for use in e.g. food engineering applications. This work focused in evaluating physical and mass transfer properties of simple poly -caprolactone nanofibers (PCL membrane), and poly ε-caprolactone nanofibers with encapsulated trypsin (E-PCL membrane), in view of their future use in a catalytic filter reactor. PCL membranes registered high hydrophobicity values, while E-PCL membranes revealed stronger mechanical properties and an increase of mass due to water incorporation. A decrease of average pore size in the range of 30% to 40% was observed for E-PCL membranes and an average pore diameter of 1/3 of the size was registered when compared to the PCL membrane; this difference was shown to be significant enough to influence the transport of larger molecules (e.g. bovine serum albumin). Release experiments of active compounds (lysozyme, bovine serum albumin and lactoferrin) were successfully described by a model which accounts for both Fick and Case II transport the linear superimposition model. Results show that the transport mechanism is influenced by the type of active compound and by membranes physical properties. ; The present study was developed under the scope of the NanoBioCats project (PTDC/CTM-POL/112289/2009), funded by the Portuguese Science and Technology Foundation (Fundação para a Ciência e a Tecnologia – FCT). This work was also supported by the COMPETE program (funded by the European Union fund, FEDER under the framework of QREN (Programa Operacional Regional do Norte (ON.2 – O Novo Norte; FEDER))) through projects NORTE-07-0124-FEDER-000028 and NORTE-07-0124-FEDER-000069. Also, the authors thank Strategic Projects PEst-OE/EQB/LA0023/2013, PEst-C/EQB/LA0006/2013 – FCOMP-01-0124-FEDER-37285 and PEst-C/QUI/UI0062/2013 – FCOMP-01-0124-FEDER-037296. The Fundação para a Ciência e Tecnologia (FCT, Portugal) through grant SFRH/BD/73178/2010