The fumigant 1,3-dichloropropene (1,3-D) is one of the most heavily used pesticides but also a suspected carcinogen. Previous research has shown that 1,3-D was rapidly transformed and detoxified by ammonium thiosulfate (ATS), a sulfur and nitrogen fertilizer. As common formulations contain cis and trans isomers at roughly equivalent ratios, this study was conducted to understand isomeric differences in thiosulfate transformation and detoxification of 1,3-D. Under the same conditions, reaction of cis-1,3-D with thiosulfate was more than three times faster than trans-1,3-D, which was correlated with a lower reaction activation energy for the cis isomer. The trans isomer was considerably more toxic to the luminescent bacteria Vibrio fisheri than the cis isomer, but the toxicity was reduced by 14 times after thiosulfate transformation. Mutagenic activity to strains of Salmonella typhimurium was observed for trans-1,3-D but was not detected after thiosulfate transformation. These results suggest that thiosulfate transformation detoxifies 1,3-D primarily by deactivating the trans isomer, and the reaction is toxicologically beneficial, as it negates the potential harmful effects of 1,3-D to the environment and human health.