The isolation of pure compounds from complex extracts is a crucial step in natural products (NPs) research. Historically, this process has been recognized to be slow and laborious. However, significant advancements have been made in isolation methods. Efficient separation conditions can now be efficiently determined at the analytical scale using high- or ultra-high-performance liquid chromatography and transferred to the preparative scale by chromatographic calculations. This ensures consistent selectivity at both scales, offering precise separation predictions. High-resolution chromatographic conditions at the preparative scale can be achieved through optimized sample preparation and dry load sample introduction. Monitoring chromatographic traces issued from ultraviolet (UV), mass spectrometry (MS), and/or universal detectors such as evaporative light-scattering detectors (ELSD) can precisely guide the isolation or trigger the collection of specific NPs with diverse structural scaffolds. These approaches can be applied across different scales depending on the amounts of NPs targeted for isolation. This chapter presents a detailed description of an isolation protocol, using the aforementioned methodologies.