Saffron is recognized as the most valuable spice worldwide, not only for its culinary applications but also for its roles in traditional medicine and pharmaceutical industries. Its high value is primarily attributed to the presence of bioactive compounds. Microencapsulation, a technique used to entrap active constituents within particles for controlled release at specific times and locations, has been shown to enhance the stability of these sensitive compounds. Among various methods, spray drying is widely employed in microencapsulation processes. In the present study, bioactive compounds of saffron were encapsulated using starch extracted from saffron corms as the wall material at concentrations of 5%, 10%, and 20% through spray drying. The physicochemical properties of the resulting powders, including water activity, particle size and distribution, as well as the retention of saffron’s major active constituents (crocin, safranal, and picrocrocin), were systematically evaluated. Scanning electron microscopy was employed to investigate the entrapment efficiency and morphological characteristics of the microcapsules. Results indicated that the sample containing 20% starch as the wall material exhibited superior microcapsule morphology compared to other formulations, with enhanced sphericity and structural integrity. Increasing the concentration of wall material was associated with a reduction in water activity (0.173), as well as a decrease in particle size to 88.7 nm, leading to the formation of stable microcapsules that prevented agglomeration during encapsulation. Additionally, higher wall material levels resulted in increased positive zeta potential values (up to +25 mV), confirming the improved stability of the encapsulated system. Encapsulation efficiency was high across all formulations, averaging 96%. Notably, microcapsules prepared with 5% wall material exhibited enhanced protective effects against degradation of saffron’s color compounds (0.56 nm). In conclusion, microencapsulation of saffron extract using starch derived from saffron corms is an effective strategy for preserving its bioactive compounds, offering promising potential for applications in food and pharmaceutical industries.