The decomposing plant materials from a green manure crop can harm seeds in several ways. First, acids and other chemicals produced during decomposition can affect germination and seedling growth. Other chemicals that are released from the plant material, especially when a Brassica green manure is used, can also reduce emergence. Finally, some pests are favored by conditions created just after a green manure is incorporated. Damping off diseases in the soil can increase rapidly and then decrease to original levels or below after a few weeks. Infestations of seed maggots are often associated with fresh decaying organic matter and so can be a risk with green manures. In most conditions, at least two weeks should separate the incorporation of a green manure and the planting of the following crops. However, there are several factors that should be considered. Decomposition will be slowed in cool soils. Small seeded crops are more affected by these conditions than large seeded crops, and the greater the amount of biomass incorporated, the longer the delay in planting should be. Fall incorporation can reduce these risks but may increase the potential for leaching of nutrients.

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