We used the horse–cyathostomin system to quantify the resilience of the nematode-bacteria interactions following an anthelmintic treatment. This matched case-control study enrolled 20 healthy and 20 naturally infected horses, whereby half received an anthelmintic drug to remove adult worms from the gut lumen without hampering the development of larval stages. Metabarcoding approaches were implemented to track faecal microbiota and cyathostomin community compositions over a 42-day time-course.