Functional ecology and biodiversity lack reference data and integrative frameworks to assess traits at different levels. Here, we integrate data from 16 field samples of complex thallose liverworts (order Marchantiales) collected from biological soil crust communities in Southern Sweden and Germany at three levels: (1) bioimaging (morphometric measurements from macro- and microscopy), (2) metabolomics (molecular computations performed on liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS), and (3) DNA marker sequencing. These data are used for a reference framework demonstrating the extraction of phenotypic and molecular traits of plants, and for generating cross-domain phylogenetic trees and diagnostic plots to assess the trait space. Our integrative data framework facilitates the systematic and standardised extraction of phenotypic and molecular traits and fosters an integration into the plant trait database TRY. Our framework helps to better assess the status and impact of global change and anthropogenic biodiversity loss of thallose liverworts within soil crusts using meta-synthesis and data integration methods, and further encourages the reuse of phenotypic and molecular traits in functional ecology and related disciplines.