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Low-resource individuals are at increased risk of obesity and cardiovascular disease (CVD), partially attributable to poor dietary patterns and dysfunctional microbiota. Dietary patterns in childhood play critical roles in physiological development and are shaped by caregivers, making caregiver-child dyads attractive targets for dietary interventions to reduce metabolic disease risk. Herein, we targeted low-resource caregiver-child dyads for a 10-week, randomized, controlled, multifaceted lifestyle intervention including: nutrition and physical activity education, produce harvesting, cooking demonstrations, nutrition counseling, and kinetic activites; to evaluate its effects on dietary patterns, CVD risk factors, and microbiome composition. Subjects in the lifestyle intervention group improved total diet quality, increased whole grain intake, decreased energy intake, and enhanced fecal elimination of the microbe-derived metabolite lithocholic acid (LCA) in contrast to control subjects. Microbiomes were highly personalized, similar within dyads, and altered by lifestyle intervention. Differential modeling of microbiome composition identified taxa associated with total diet quality, whole grain intake, and LCA elimination including recognized fiber-degrading bacteria such as Subdoligranulum, and bile acid metabolizing organisms like Bifidobacterium. Inclusion of taxa identified in diet and metabolite modeling within blood pressure models improved prediction accuracy of microbiome-blood pressure associations. Importantly, microbiota-blood pressure relationships were shared between dyads, implying shared host-microbiota responses to lifestyle intervention. Overall, these outcomes provide insight into mechanisms by which dietary interventions impact the gut-cardiovascular axis to reduce future CVD risk. Registered at clinicaltrials.gov: NCT05367674