Accurate vegetation mapping is essential for monitoring biodiversity and managing habitats, particularly in the context of increasing environmental pressures and conservation needs. Ground truthing plays a crucial role in ensuring the accuracy of supervised remote sensing maps, as it provides the high-quality reference data needed for model training and validation. However, traditional ground truthing methods are labor-intensive, time-consuming and restricted in spatial coverage, posing challenges for large-scale or complex landscapes. The advent of drone technology offers an efficient and cost-effective solution to these limitations, enabling the rapid collection of high-resolution imagery even in remote or inaccessible areas. This study proposes an approach to enhance the efficiency of supervised vegetation mapping in complex landscapes, integrating Multivariate Functional Principal Component Analysis (MFPCA) applied to the Sentinel-2 time series with drone-based ground truthing. Unlike traditional ground truthing activities, drone truthing enabled the generation of large, spatially balanced reference datasets, which are critical for machine learning classification systems. These datasets improved classification accuracy by ensuring a comprehensive representation of vegetation spectral variability, enabling the classifier to identify the key phenological patterns that best characterize and distinguish different vegetation types across the landscape. The proposed methodology achieves a classification accuracy of 92.59%, significantly exceeding the commonly reported thresholds for habitat mapping. This approach, characterized by its efficiency, repeatability and adaptability, aligns seamlessly with key environmental monitoring and conservation policies, such as the Habitats Directive. By integrating advanced remote sensing with drone-based technologies, it offers a scalable and cost-effective solution to the challenges of biodiversity monitoring, enabling timely updates and supporting effective habitat management in diverse and complex environments.