A 2-yr study was conducted on a loamy sand soil to compare short-term persistence of ammonium-N in an annual (ACS) and a perennial (PCS) cropping system following pig manures application as a possible explanation for the reduced nitrate leaching from perennial forage grasses. In spring 2014 and 2015, nitrogen-based application rates of liquid (LPM) and solid (SPM) pig manure were broadcast on PCS and ACS plots with incorporation of the manures for ACS plots alone. Following manure applications, soil samples were taken at 0–15 and 15–30 cm depths seven times (2014) and six times (2015) over 2–3 wk period for ammonium-N and nitrate-N concentrations. Ammonium-N (0–15 cm) with LPM peaked 4 d after manure application in ACS (18–29 kg ha^-1) and PCS (50–74 kg ha^-1) in both years. In both years, persistence of ammonium-N at 7 d was 46%–77% in LPM-amended PCS and 8%–14% in LPM-amended ACS. Ammonium-N measured in SPM-amended ACS and PCS was low after manure application in both years. There was lower accumulation of nitrate-N in PCS than ACS of LPM- and SPM-amended treatments in both years. The greater persistence of ammonium-N in the LPM-amended PCS than ACS coupled with lower percentage increase in nitrate-N in the PCS may account for lower nitrate leaching previously observed for perennial forage grasses at the study location.