Ammonia (NH3) emissions from animal agriculture can cause eutrophication of water ecosystems and are precursors to secondary particulate matter (PM2.5). NH3 emissions from stored swine manure represent nutrient loss affecting the fertilizing value of manure. The short-term emission bursts occur when farmers agitate manure before emptying storage and fertilizing fields. There is no proven technology to mitigate gaseous emissions during agitation, while the hazards of acute releases (e.g., H2S) are well-known. Biochar mitigates NH3 emissions from manure over the long-term. The objective of this research was to evaluate the mitigation of acute NH3 emissions during/after agitation. Two biochars, highly alkaline and porous (HAP from corn stover) and red oak (RO), were tested. The 6 and 12 mm-thick layers of biochar powder were surficial applied followed by 3 min agitation. NH3 concentrations were measured before/during/after agitation. Mitigation was assessed by comparing: (i) the maximum (peak) flux, (ii) total emission (from agitation start till NH3 concentration returned to the before-agitation), and (iii) the total emissions during agitation. The 12 mm HAP significantly (p < 0.05) reduced (i–iii) by 63, 70, and 85%, respectively. The 6 mm HAP significantly reduced (i–iii) by 76, 75, and 78%, respectively. The 12 mm RO significantly reduced (i–iii) by 9, 53, and 57%, respectively. The 6 mm RO significantly reduced (i–iii) by 61, 86, and 63%, respectively. The NH3 emission kinetics model confirmed that a 6 mm dose was just as effective as the larger dose. More research is needed to optimize and scale-up mitigating emissions and retention of nutrients in manure with biochar.