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Nematode-resistant cover crops can suppress populations of plant-parasitic nematodes. Samples of a loamy and a sandy loam soil were collected from two sugar beet fields in Lower Saxonia, northern Germany (&#8220;Jeinsen&#8221; and &#8220;Gross Munzel&#8221;) to measure the effects of cover cropping on the population genetic structure and infectivity of <i>Heterodera schachtii</i> as well as the composition of soil microbial communities. These fields allowed for a comparison of cover cropping with Brassica species resistant to <i>Heterodera schachtii</i> to fallow. In a series of radish bioassays with <i>H. schachtii</i> populations from Jeinsen and Gross Munzel, ratios of second-stage juveniles in roots per eggs in soil were higher in soil from under Brassica cropping than from under fallow. In denaturing gradient gelelectrophoresis, profiles of the parasitism gene <i>vap1</i> differed between Brassica and fallow treatments in both populations. At Gross Munzel, microbes of soils and within nematode cysts differed between Brassica and fallow areas. Specifically, the frequency and occurrence of isolates of <i>Pochonia chlamydosporia</i> and <i>Exophiala salmonis</i> were lower within the cysts from Brassica than from fallow treatments. Overall, cover cropping with resistant Brassica species affected the bacteria and fungi infecting the cysts and subsequently, the infectivity of the <i>H. schachtii</i> population. Cover crop effects on nematode virulence (<i>vap1</i> gene) and microbial colonization of the cysts could affect long-term nematode population dynamics.