A new silk fibroin-based nanoparticles (FNPs) have been successfully developed utilizing crosslinker EDC (EDC-FNPs) or cationic polymer poly(ethyleneimine) (PEI-FNPs). All developed crosslinked FNPs show a similar spherical particle size of similar to 300 nm. Depending on the amount of EDC or the addition of PEI, the zeta potential could be controlled favorably and range from - 15 mV to + 30 mV. Particle structures and crystallinity index are determined and compared using different techniques; X-ray diffraction (XRD), Fourier-transformed infrared spectroscopy (FT-IR), differential scanning calorimetry and nuclear magnetic resonance (NMR). The most reliable crystallinity calculation methods are based on FT-IR and NMR. The degree of fibroin crystallinity increases with increasing EDC content, whereas PEI reduces it. Exceptionally, XRD shows a reverse order of crystallinity due to the inability to detect short-range ordered structures. Proposed schematic particle structures match all experimental data. In conclusion, the crosslinked fibroin-based nanoparticle properties could be manipulated by using carbodiimide or PEI crosslinkers. In addition, both EDC-FNPs and PEI-FNPs showed high potential as a drug delivery system.