Halloysite nanotube (HNT)-reinforced alginate-based nanofibrous scaffolds were successfully fabricated by electrospinning to mimic the natural extracellular matrix (ECM) structure which is beneficial for tissue regeneration. An antiseptic drug, cephalexin (CEF)-loaded HNT, was incorporated into the alginate-based matrix to obtain sustained antimicrobial protection and robust mechanical properties, the key criteria for tissue engineering applications. Electron microscopic imaging and drug release studies revealed that CEF had penetrated into the lumen space of the HNT and also deposited on the outer walls, with a total loading capacity of 30 wt %. Moreover, the diameter of alginate-based nanofibers of the scaffolds ranged from 40 to 522 nm with well-aligned HNTs, resulting in superior mechanical properties. For instance, the addition of 5% (w/w) HNT improved the tensile strength (σ) and elastic modulus by 3-fold and 2-fold, respectively, compared to those of the alginate-based scaffolds without HNT. The fabricated scaffolds exhibited remarkable antimicrobial properties against both Gram-negative and Gram-positive bacteria, and the cytotoxicity studies confirmed the nontoxicity of the fabricated scaffolds. Drug release kinetics showed that CEF inside HNTs diffuses within 24 h and that the diffusion of the drug is delayed by 7 days once the CEF-loaded HNTs are incorporated into the alginate-based nanofibers. These fabricated alginate-based electrospun scaffolds with enhanced mechanical properties and sustained antimicrobial protection hold great potential to be used as artificial ECM scaffolds for tissue engineering applications.