Biodiversity loss on agricultural land is a major concern. Comprehensive monitoring is needed to quantify the ongoing changes and assess the effectiveness of agri-environmental measures. However, current approaches to monitoring biodiversity on agricultural land are limited in their ability to capture the complex pattern of species and habitats. Using a real-world example of plant and habitat monitoring on Swiss agricultural land, we show how meaningful and efficient sampling can be achieved at the relevant scales. The multi-stage sampling design of this approach uses unequal probability sampling in combination with intermediate small-scale habitat sampling to ensure broad representation of regions, landscape types, and plant species. To achieve broad coverage of temporary agri-environmental measures, the baseline survey on permanent plots is complemented by dynamic sampling of these specific areas. Sampling efficiency and practicality are ensured at all stages of sampling through modern sampling techniques, such as unequal probability sampling with fixed sample size, self-weighting, spatial spreading, balancing on additional information, and stratified balancing. In this way, the samples are well distributed across ecological and geographic space. Despite the high complexity of the sampling design, simple estimators are provided. The effects of stratified balancing and clustering of samples are demonstrated in Monte Carlo simulations using modelled habitat data. A power analysis based on actual survey data is also presented. Overall, the study could serve as a useful example for improving future biodiversity monitoring networks on agricultural land at multiple scales.