Objectives This study aimed to clarify the effects and underlying mechanisms of organic fertilizer substitution for chemical fertilizer (organic substitution) on trace element contents in Lou soil and grains and crop yield, so as to provide a scientific basis for enhancing micronutrient availability in Lou soil and achieving high crop yields with improved quality.

Methods A long-term organic substitution field experiment (initiated in 2014) was conducted in a winter wheat-summer maize rotation at the National Agricultural Experimental Station for Soil Quality in Yangling. Soil and crop samples were collected in 2024 following crop harvest from plots under the following treatments: no fertilizer control (CK), chemical fertilizer only (NPK), and substitution of 25%, 50%, 75%, and 100% of chemical nitrogen fertilizer with organic fertilizer (25%M, 50%M, 75%M, and 100%M). Soil bulk density, organic matter and nutrient contents, and enzyme activities were analyzed. The contents of Fe, Mn, Cu, and Zn in grains were analyzed, and crop yield was measured.

Results Fertilization significantly increased soil cation exchange capacity (CEC), organic matter, total N, total P, available P, available K, and cellobiohydrolase (CBH) activity, and these increases were greater at higher organic substitution ratios, but fertilization did not significantly affect soil bulk density. Compared with CK, chemical fertilizer alone generally maintained soil total and available Fe, Mn, Cu, and Zn contents, whereas organic substitution significantly increased soil total contents of Fe, Mn, Cu, and Zn by 13%, 5%, 17%, and 32%, respectively, and available contents by 23%, 32%, 25%, and 244%, respectively, with increasing trends as the organic substitution ratio increased. Compared with CK, both NPK and organic substitution mainly increased the humic acid-bound, Fe-Mn oxide-bound, and strongly bound fractions of Fe, Mn, Cu, and Zn, showing a clear dose effect of organic fertilizer application. Compared with CK, NPK significantly increased wheat and maize yields by 268% and 126%, respectively, and organic substitution significantly increased wheat and maize yields by 108%–268% and 129%–141%, respectively. Wheat yield was higher under NPK and 25%M than under 50%M, 75%M, and 100%M, whereas maize yield did not differ significantly among treatments. Compared with CK, NPK maintained or slightly increased grain Fe, Mn, Cu, and Zn contents in wheat and maize, whereas organic substitution increased Fe, Mn, Cu, and Zn contents of wheat grain by 32%, 40%, 75%, and 30% on average, respectively; the increases in maize grain trace-element contents were slightly greater overall than in wheat, and all increased with increasing substitution ratio. Furthermore, both soil available trace-element contents and grain trace-element contents were significantly and positively correlated (P<0.05) with soil organic matter, CEC, CBH activity, and N, P, and K nutrient contents.

Conclusions Partial substitution of chemical fertilizer with organic fertilizer increased soil CEC, organic matter, and N, P, and K nutrient contents, as well as enzyme activity, significantly improved soil trace-element availability, and consequently increased wheat and maize yields and grain trace-element contents. As the substitution ratio increased, soil trace-element availability and grain trace-element contents tended to increase, but wheat yield decreased significantly and maize yield showed no significant change. At an organic substitution ratio of 25%, wheat yield was maintained at a high level while Lou soil and grain trace-element contents increased to a certain extent; therefore, a 25% organic substitution ratio is an effective measure for synergistically achieving high crop yield, grain trace-element fortification, and soil fertility improvement in the wheat–maize rotation system on Lou soil in the Guanzhong Plain.