Electrospinning is a widely used technology for micro-and nanofibers production. However, when in situ fibers deposition or immobilization of specific agents is required, solution blow spinning (SBS) is a safer alternative. In this work, SBS system was used to produce core-shell fibers with potential use in bioactive agent delivery. Two biodegradable polymers (poly(lactic acid) -PLA and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) -PHBV) were processed with different working distances and air pressure to evaluate the influence of these variables as well as the characteristics of polymers on the fiber morphology. PHBV fibers present the best morphology with fewer defects and beads, although these fibers show larger diameters (from 2.03 to 2.27 μm) compared to PLA fibers (from 0.54 to 2.03 μm). Moreover, deposition of PHBV fibers is not significantly affected by the processing variables, indicating stability under SBS processing. PHBV is firstly used as a matrix to encapsulate hydrophilic bioactive in core-shell structure via SBS. This structure allows the sustained release of lipase even after 14 days, evidencing the efficiency of the core-shell fibers in producing controlled release systems. Core-shell aligned fibers with a reduced diameter (from 3.07 to 1.42 μm) are produced replacing the static target with a rotating collector.