In this work, the effect of fabrication parameters on silk fibroin (SF) nonwovens obtained by electrospinning were evaluated. Additionally, the relationship between secondary structures and thermal stability of the protein materials, with morphological characteristics of nonwovens obtained were analyzed. Silk fibroin in formic acid solution at 10% w/w was electrospun at 8 cm varying the ratio voltage/distance and flow rate. The nonwovens morphology was observed by Scanning Electron Microscopy (SEM) and fibers diameter were determined with ImageJ software. The changes in the secondary structure of silk fibroin before and after electrospinning were studied by Fourier Transform Infrared Spectroscopy (FTIR) and Differential Scanning Calorimetry (DSC) to evaluate the effect of electrospinning process in the molecular structure of SF. Optimum morphology of SF nonwovens were obtained at R = 1 kV/cm and low flow rate, these process parameters were related to higher contents of crystalline structures in the materials. Results showed that SF nonwovens obtained under controlled process parameters hold great potential to be utilized in several applications such as tissue engineering.