Purpose The balance of micronutrients in soils is important in nutrient use efficiency, environmental protection and the sustainability of agro-ecological systems. The deficiency or excess of micronutrients in the plough layer may decrease crop yield and/or quality. Therefore, it is essential to maintain appropriate levels of micronutrients in soil, not only for satisfying plant needs in order to sustain agricultural production but also for preventing any potential build-up of certain nutrients. Materials and methods A long-term fertilizer experiment started in 1969 at Central Rice Research Institute, Cuttack, Odisha, India. Using this experiment, a study was conducted to analyze the balance of micronutrients and their interrelationship. The experiment was composed of ten nutrient management treatments viz. control; nitrogen (N); N + phosphorus (NP); N + potassium (NK); nitrogen, phosphorus and potassium (NPK); farmyard manure (FYM); N + FYM; NP + FYM; NK + FYM; and NPK + FYM with three replications. Micronutrients in soil (total and available), added fertilizers and organic manures and in rice plant were analyzed. Besides, atmospheric deposition of the micronutrients to the experimental site was also calculated. A micronutrient balance sheet was prepared by the difference between output and input of total micronutrients. Results and discussion Application of FYM alone or in comb i n a t i o n w i t h c h e m i c a l f e r t i l i z e r i nc r e a s e d th e diethylenetriamine pentaacetate (DTPA)-extractable Fe, Mn and Zn over the control treatment. The treatment with NPK + FYM had the highest soil DTPA-extractable Fe, Mn, Zn and Cu after 41 years of cropping and fertilization. Application of chemical fertilizers without P decreased the DTPA-extractable Zn over the control while the inclusion of P in the fertilizer treatments maintained it on a par with the control. The application of P fertilizer and FYM either alone or in combination significantly increased the contents of total Fe, Mn, Zn and Cu in soil mainly due to their micronutrient content and atmospheric depositions. A negative balance of Zn was observed in the N, NP, NK and NPK treatments, while a positive balance observed in the remaining treatments. The balance of Mn was negative in all the treatments, due to higher uptake by the rice crop than its addition. Conclusions Long-term application of chemical fertilizers together with FYM maintained the availability of micronutrients in soil and, thus, their uptake by rice crop.