PURPOSE: This study evaluates manure and chemical fertilizer effects on micronutrient (Fe, Mn, Cu, and Zn) content and availability in crops. METHODS: Seven treatments were selected, including three conventional fertilization treatments (NP, horse manure (M), and NP plus M (NPM)), three corresponding double rate fertilization (N2P2, M2, and N2P2M2), and a CK. Soil samples were collected and separated into four aggregates by wet-sieving in September 2009. Corn samples were collected and analyzed simultaneously. RESULTS: Treatment N2P2 increased DTPA extractable Fe, Mn, and Cu in soil by 732%, 388%, and 42%, whereas M2 decreased the corresponding values by 26%, 22%, and 10%, respectively, compared to CK. DTPA extractable Zn in soil and Zn in corn grain were higher in the M and M2 treatments than in the other treatments, and DTPA Zn was significantly correlated with soil organic carbon (SOC) in large macroaggregate, microaggregate, and silt + clay fractions. The Mn concentrations in corn stalks and grain were significantly correlated with DTPA extractable Mn in bulk soil and microaggregates, and Zn in stalks were significantly correlated with DTPA Zn in bulk soil, microaggregates, and large macroaggregates. CONCLUSIONS: Long-term application of horse manure could increase soil Zn availability and uptake by corn, possibly due to its activation by SOC. In contrast, chemical fertilizer application increased DTPA extractable Fe, Mn, and Cu in soil by reducing soil pH. Our results also suggest that Mn uptake by corn originated mainly in microaggregates, whereas Zn in crops was primarily sourced from large macroaggregates and microaggregates.