Background <p>Egyptian clover (<i>Trifolium alexandrinum</i> L.) is a high-yield and high-nutrition legume forage crop. However, traditional natural drying methods are inefficient, cause severe nutrient loss, and pose a high risk of fungal contamination. Little is known about the dynamic changes in its hay quality, fungal community, and microstructure during storage with the addition of chemical additives.</p> Results <p>This study aimed to evaluate the effects of ten chemical additives (a natural sun-drying control [CON] and different mass fractions of NaHCO₃ [1%, Na1; 2%, Na2; 3%, Na3], K₂CO₃ [1%, K1; 2%, K2; 3%, K3], and CaCO₃ [1.5%, Ca1; 2%, Ca2; 2.5%, Ca3]) × four storage times (0, 30, 60, and 90 d) on the dehydration efficiency, nutritional quality, and fungal communities at 0 and 90 d of storage in Egyptian clover hay. The results showed that K3 and Na3 significantly shortened the drying time from 72.0&#xa0;h to 54.7&#xa0;h (<i>P</i> &lt; 0.0001), representing a 24.0% reduction compared to CON. Ca3 significantly decreased the leaf loss rate by 26.1% (<i>P</i> = 0.006) relative to CON, and K1 and Ca3 significantly increased the crude protein content by 27.6% and 26.8%, respectively (<i>P</i> &lt; 0.0001). After 90 d of storage, Na3 had the lowest total fungal count (4.34 log₁₀ CFU g^− 1 FM), effectively inhibited the proliferation of spoilage-associated fungal genera such as <i>Aspergillus</i> and <i>Wallemia</i>, and altered the dominant fungal community dominated by <i>Vishniacozyma</i> and <i>Alternaria</i>. Grey relational analysis confirmed that K3 had the highest comprehensive relational grade (0.809) and best overall performance.</p> Conclusions <p>The results suggest that 3% K₂CO₃ is a promising practical additive for Egyptian clover hay production, mainly by accelerate dehydration through cuticle-related physical changes and by helping maintain nutritional quality and fungal community characteristics during storage.</p>