•Si fertilization attenuates salt stress on onion plants.•Si fertilization increases onions grown and yield under salt stress conditions.•Si fertilization improves onions postharvest quality in salt stress conditions.•Si fertilization increases onions organic acid in salt stress conditions. Salinity limits agricultural yield in the arid and semi-arid regions of the world. Silicon (Si) benefits plants under abiotic stresses. However, Si fertilization in the yield of onion plants under salt stress are less well known. We conducted a field experiment to evaluate Si fertilization in onion yield, physiology and postharvest quality irrigated with saline water. The experiment was designed in randomized complete blocks, with four replicates, and treatments were arranged in split plots. The plots had four water electrical conductivity (0.65, 1.7, 2.8 and 4.1 dS m−1) and the subplots had five Si levels (0, 41.6, 83.2, 124.8 and 166.4 kg ha−1 of Si), in the form a diatomaceous earth-based fertilizer derived from the species Melosira granulata. Waters high salinity reduced onion yield and bulb fresh mass, and increasing small bulbs (<50 mm) production. Waters high salinity hampered onion plants membrane instability index, relative water content and contents of total chlorophyll, and carotenoids. Waters high salinity too hampered onion firmness, pH, soluble solids concentration, and SS/TA ratio. Si fertilization increased onion yield, bulb fresh mass and production of large bulbs (≥ 50 mm), and saline stress attenuation occurred up to 2.8 dS m−1. Si fertilization improved onion plants chlorophylls, carotenoids, total sugars, soluble solids, ascorbic acid, and pyruvic acids content. Si fertilization promoted onions acclimatization to salt stress, because increasing the synthesis of soluble sugars, ascorbic acids, and thio-compounds identifiable in PyA. Therefore, we recommend 78.5 kg ha−1 of Si for onion plants under saline stress conditions.