Abstract Despite the major role that insect pollinators play in crop production, agricultural intensification drives them into decline. Various conservation measures have been developed to mitigate the negative effects of agriculture on insect pollinators. In a novel comparison of the efficacy of three conservation measures on honeybee colony growth, we monitored experimental honeybee colonies in 16 landscapes that comprised orthogonal gradients of organic agriculture, annual flower strips and perennial semi‐natural habitats. Using structural equation modelling, we assessed the effects of conservation measures on the prevalence of 11 parasites, Varroa destructor loads and their collective impact on colony growth. Increasing area coverage of perennial semi‐natural habitat related to higher V. destructor load and indirectly to lower colony growth. Increasing area of annual flower strips was associated with lower V. destructor load and indirectly with higher colony growth. Increasing area of organic farming related to lower parasite richness and also directly to improved colony growth. Synthesis and applications: Landscape features can affect pollinators directly through the provision of food resources and indirectly through modulation of parasite prevalence. To promote honeybee colony health in agro‐ecosystems, our results suggest that organic agriculture and annual flower strips should be prioritized conservation measures. Landscape management should consider the merits and demerits of different measures to sustain healthy populations of pollinators in agro‐ecosystems.