Organic amendment is a traditional practice for rehabilitating saline patches in north-east Thailand, but organic matter is known to enhance methane emission. However, a high degree of salinity might mitigate methane emission. The objective of the present study was to quantify the effects of salinity and organic amendments on methane emission from rain-fed paddy fields exposed to increasing salinity. A paddy field on a salt-affected Typic Natraqualfs was selected. Eighteen experimental plots were located in two randomized complete block designs placed inside and outside a saline patch. Each design of nine plots presented three replicates of two different organic amendments and a control treatment without organic amendment. During the rainy season the soil electrical conductivity, measured with an electromagnetic conductivity meter (ECEM), was greater than 300 mS m−1 inside the saline patch, whereas outside the saline patch the values were lower than 200 mS m−1. Rice straw (6.25 t ha−1) and cow manure (8.99 t ha−1), representing similar amounts of carbon, were incorporated. Methane emission from the soil, EC1:5 and soil redox potential (Eh) were monitored during the rice-growing season. High methane emission was mostly associated with low Eh, 48% of the Eh measurements were between −100 mV and −200 mV. In the saline patch, the average methane emission ranged from 251 to 334 mg CH4 m−2 day−1; outside the saline patch the values had a wider range from 209 to 544 mg CH4 m−2 day−1. The addition of rice straw or cow manure significantly enhanced methane emission by an approximate factor of 2.5 outside the saline patch, but did not significantly increase methane emission inside the saline patch. The attenuating effect of salinity on methane emission was particularly strong at the beginning of flooding during the first 20 days after transplanting and at the end of flooding (from 54 days after transplanting). When applied to saline patches, organic amendment did not significantly enhance methane emission in the first year.