Several Allium cepa L. varieties, representing a versatile set of vegetables widely utilized by consumers, are appreciated for their bioactive properties, including antimicrobial, anticarcinogenic, and antioxidant capacities. The aim of this study is to compare the morphometric characteristics and biochemical profiles of four cultivars of A. cepa, two of them represented by the perennial Sicilian landrace "Cipudda agghiarola" (Allium × proliferum (Moench) Schrader), widely known as the Egyptian walking onion (WO), and by the landrace "Cipudduzza" belonging to the variety known as aggregatum (ON), which were compared with two commercial cultivars of A. cepa var. cepa (onion), Stoccarda (OS) and Rossa Carmen (OR). The experimental trial was conducted in Catania (Sicily), following organic growing practices. The randomized complete block experimental design was adopted with one experimental factor, the genotype (GE) effect. The harvested plants were characterized for their main morphometric parameters, according to the International Plant Genetic Resources (IGPR) descriptors. The biochemical activity was assessed by analyzing the total phenolic content (TPC) and the total flavonoid content (TFC). The antioxidant capacity was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC). The sugar profile (total sugars, sucrose, glucose, fructose, and fructooligosaccharides-FOS) and the volatile compounds by headspace-gas chromatography/mass spectrometry (HS-GC/MS) were also determined. The OR bulb exhibited the highest TPC (16.3 mg GAE/g d.w., p < 0.01) and TFC (8.5 mg QE/g d.w., p < 0.01), with the highest antioxidant capacity measured by the FRAP (27.1 µmol TE/g d.w., p < 0.01) and DPPH assays (46.2 µmol TE/g d.w., p < 0.01). The ON bulb showed the highest ORAC value (209 µmol TE/g d.w., p < 0.01). Generally, the bulbs were richer in sugars (584 mg/g d.w., p < 0.01) than the leaf blade (239 mg/g d.w., p < 0.01), except for OR. Significant interaction between the genotype and plant organ was noted in the volatile compound profiles (p < 0.05) except for total ketones and carboxylic acids, where higher content was observed in the leaf blade compared to the bulb, regardless of the genotype. These findings highlight WO's potential for use in ready-to-eat products, enhancing its market value.