Salinity is a major constraint for crop productivity as it reduces agricultural land area. This problem can be ameliorated by the application of organic materials such as manure, which plays an important role in supporting plant growth and reducing soil toxicity by binding toxic compounds. The purpose of this study is to analyse the effect of manure in overcoming the impact of salt stress on shallots. Here Randomised Block Design (RBD) consisting of 2 factors and 3 replications was used. The first factor is salinity levels (0, 50, 100, and 150 mM), and the second is manure doses (0, 10 and 20 t ha-1). This study finds that the application of 20 t ha-1 of manure decreases the shallot’s leaf tissue thickness, but the 50 mM of salinity significantly increases it. Then, the application of 20 t ha-1 of manure increases the shallot’s number of tillers and bulbs, while the 100 mM of salinity significantly decreases its number of tillers. The application of 10 t ha-1 of manure decreases the proline and flavonoids content of the plant’s leaves. In addition, plants treated and not treated with manure under 50 mM of salinity have higher proline and flavonoids levels in their leaf. Therefore, shallots can grow under salinity conditions if manure is applied.