Magnetically responsive polymer composites have great potential for use in diverse biomedical applications. In this study, composite biomaterials consisting of silk fibroin (SF) and superparamagnetic iron oxide nanoparticles (SPIONs) were fabricated by the electrospinning method. Two different methods were employed to incorporate the SPIONs into the SF nanofibers. In the first encapsulation method (M1), SPIONs (1.0, 3.0, and 5.0 wt%) were initially included in the electrospinning solution. In the second dip-coating method (M2), electrospun SF nanofiber mats were immersed in the aqueous suspensions of SPIONs (10, 30 and 50% v/v). Then, the pure and composite silk fibroin composite mats were comparatively evaluated for their morphological, chemical, magnetic, mechanical and in vitro biological properties, by using a number of methods including SEM, TEM, FTIR, XRD, EDS, VSM, TGA, mechanical tensile tests, as well as by indirect in vitro cytotoxicity and in vitro hemocompatibility analyses. Overall findings suggested that, while M1 nanofiber mats could be a suitable candidate for use in tissue engineering as a magnetically responsive cytocompatible scaffold, the M2 nanofiber mats perhaps could be more appropriate as an interface for triggering the in vitro stem cell differentiation and/or biosensor applications.