A microwave‐based process to control invasive species (seeds and adult stages) in the field prior to plant community restoration is currently under development. We investigated the effect of four microwave treatment pairings of Power × Duration (2kW4min, 4kW2min, 2kW8min, and 4kW4min) on seedling emergence of (1) an abandoned field seed bank used as a model for various plant species and (2) seeds of three species invasive in Europe: Datura stramonium (Jimson weed), Reynoutria × bohemica (Bohemian knotweed), and Solidago gigantea (Giant goldenrod). In addition, we assessed whether nontreated seeds of these three invasive species could germinate on microwave‐treated soils. As microwave soil heating usually leads to nonhomogeneous temperatures within a sample, we also assessed whether the position of seeds in the soil during microwave treatment (center vs. edges) impacted seedling emergence. Results show that the most intensive microwave treatments (2kW8min and 4kW4min), enabling the soil to reach 85°C, are highly effective in inhibiting seedling emergence of invasive species and the seed bank. The 2kW8min treatment, combining lowest power and longest exposure, is the most effective, reducing seed bank seedling emergence by 98% compared to control. The results also reveal a species‐specific response to heat, and lower microwave effectiveness on seeds located at the soil surface, which may explain the incomplete effectiveness of intensive treatments. Our results also suggest that prior microwave soil treatment does not prevent a considerable proportion of newly arrived invasive species seeds from germinating, suggesting that this method should be followed by restoration of native plant cover.