It is known that organic nitrogen (N) may modify uptake and toxicity of metals but direct metabolic and microbial comparison of various organic N sources is not available. We therefore studied comparative impact of additional N sources (nitrate, urea or allantoin as 1 mM of N for each compound in addition to 15 mM of inorganic N in the Hoagland solution) on Cd toxicity and microbial activity in common crop cucumber. Organic N significantly elevated growth, chlorophyll content and photosynthetic activity under Cd excess in comparison with inorganic N though the impact on Cd uptake was negligible. Both organic N compounds also affected accumulation of mineral nutrients, total N, amino acids and protein content in Cd-stressed plants. Among organic acids, mainly allantoin and partially urea affected accumulation of citrate and tartrate. The most notably, we detected that allantoin was decomposed even within 24 h by microbes into the urea but it significantly elevated rhizosphere microbial activity. All these data indicate that allantoin is metabolized by plants into the urea and that it affects microbes mainly in the rhizosphere, which could contribute to amelioration of Cd toxicity.