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Steam disinfestation is an ecologically less harmful alternative to synthetic chemical fumigants such as methyl bromide, which is being phased out of use due to its ozone-depleting properties. Although previous studies have characterized the effects of steaming on targeted pests, soil microorganisms, including beneficial ones, may be strongly influenced by this agricultural practice, since: (1) high temperature disturbs most soil microorganisms; and (2) disinfestation-induced changes in the soil environment can indirectly affect soil microbiota. The impact of soil disinfestation on functional bacterial communities was evaluated particularly in view of their role in nitrogen cycling. The short-term effects of steam disinfestation on heterotrophic bacteria, denitrifying and nitrifying bacteria, and their ability to recover after this disturbance were examined by surveying the enzyme activity, size and genetic structure of each community. Our results show that: (1) steaming immediately induced significant decrease in community activity and size, and changes in community composition, nitrifying bacteria being mostly affected; (2) abundances of each community reached values equal or higher than those observed in control soil within 15–60 days after steaming, but community structures remained very different as compared to those in control soil; and (3) for each activity, no complete recovery was observed after the disturbance: substrate induced respiration and denitrification increased but remained lower in steamed soil, whereas nitrification was not detectable after 62 days. Our results show that these effects of steaming on key soil functional communities can have important, long-lasting implications for nitrogen cycle that should be taken into account when evaluating the influence of such an agricultural practice.