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SummaryFumigants, such as 1,3-dichloropropene and chloropicrin, have become key to pre-plant pest management in almond production. Whilst the use of these fumigants has become increasingly restricted due to human health concerns, less is known about their below-ground non-target effects in orchards and how nematode communities recover from fumigation over time. In this study, replicated trials compared 1,3-dichloropropene + chloropicrin to non-treated controls in two almond orchards in California, USA. Nematode communities, nematode indices and nematode metabolic footprints were quantified soon after fumigation and for 2 years afterwards. Fumigation reduced the Herbivore Metabolic Footprint in year 1, and populations of Pratylenchus vulnus in year 3. Fumigation also reduced populations of larger omnivores and predators, resulting in lower levels of the Structure Index at one site. Populations of fungal-feeding nematodes were more adversely affected by fumigation than bacterial-feeding nematode populations. At both sites, fumigation still influenced nematode community composition 2 years after treatment application.