Abstract Fall applied liquid swine ( Sus scrofa domesticus ) manure (LSM) can lead to economic and environmental concerns due to potentially enhanced NO 3 loss. Objectives of this study were to evaluate LSM application timing and use of Instinct nitrification inhibitor, and compare to anhydrous ammonia (AA). Treatments were a no‐N control, AA (without Instinct), and LSM with three Instinct rates applied each of 3 yr on October 1 (early fall) and November 1 (late fall). The effect of Instinct was inconsistent. Instinct increased soil NH 4 –N concentrations in fall (only early fall LSM application) and spring sampled LSM injection zones. However, in the late spring Instinct had no effect to minimal positive effect on soil inorganic–N, and the high rate was not more effective than the low rate. Corn ( Zea mays L.) canopy normalized difference vegetative index (NDVI) was not influenced by Instinct or different between N source, and greatest with late fall N application. Across years, Instinct increased corn grain yield only when early fall applied with the low rate. However, LSM with Instinct had lower yield compared to AA. Waiting to apply N in late fall provided increased inorganic N retention, and with LSM higher corn yield. Based on this study, AA was a better fall applied N source compared to LSM with or without Instinct. A decision to use Instinct with LSM must weigh cost of the inhibitor against other options, such as delayed fall or spring application, or use of AA.