Chickpea grains may represent an alternative to soybean meals and energetic concentrates in animal feeding, as their nutritional value can help to increase the sustainability of livestock systems. Unfortunately, the presence of bioactive compounds with anti-nutritional effects can prevent its direct use, especially in mono-gastrics. It is known that the synthesis of these compounds depends on genetic expression, which is also influenced by growth conditions. The objective of this two-year study was to assess the effect of sowing date (winter versus spring) and seeding rate (70 versus 110 seeds m−2) on the accumulation of soluble carbohydrates, α-galactosides, trypsin inhibitors, and inositol phosphates in the grains of two Kabuli cultivars, in the Mediterranean climate. The results showed that seeds collected from winter sowing contained more trypsin inhibitors than those seeded in spring (+ 4%, on average), reaching values between 16.1 and 18.6 TIU mg protein−1. The seeding rate affects only the α-galactosides content, which increases (+9%) at lower densities (70 seeds m−2). These findings suggest that agronomic management can be used to modulate the content of some anti-nutritional factors in the seeds, even though the genetic characteristics and phenotypic expression, in relation to the climatic conditions, seem to deeply affect the content of all the bioactive compounds investigated.