Research Highlights: This is the first approach that integrates biodiversity data into Mapping and Assessment of Ecosystem and their Services (MAES) implementation and natural capital accounting process, at the national scale, using an extensive vascular plant dataset for Greece. Background and Objectives: The study aims to support the MAES implementation in Greece, by assessing, as a pilot, the woodland and forest ecosystem type; the targets of the study are: (a) Identify and map ecosystem type extent; (b) identify ecosystem condition using biodiversity in terms of plant species richness (i.e., total, ecosystem exclusive, endemic, ecosystem exclusive endemic diversity); (c) develop ecosystem asset proxy indicators by combining ecosystem extent and ecosystem condition outcomes; (d) identify shortcomings; and (e) propose future steps and implications for the MAES implementation and natural capital accounting, based on biodiversity data. Materials and Methods: Following the national European Union’s and United Nations System of Environmental Economic Accounts-Experimental Ecosystem Accounting (SEEA-EEA) guidelines and the adopted National Set of MAES Indicators, we developed a set of four proxy ecosystem asset indicators to assess ecosystem types with respect to ecosystem area extent and ecosystem condition. This was as interpreted by its plant diversity in terms of species richness (total, ecosystem exclusive, endemic, and ecosystem exclusive endemic diversity). Results: The results revealed that when indicators use well-developed biodiversity datasets, in combination with ecosystem extent data, they can provide the baseline for ecosystem condition assessment, ecosystem asset delineation, and support operational MAES studies. Conclusions: The relation among biodiversity, ecosystem condition, and ecosystem services is not a linear equation and detailed, fine-scale assessments are needed to identify and interpret all aspects of biodiversity. However, areas of importance are pinpointed throughout Greece, and guidance is provided for case-study selection, conservation strategy, and decision-making under the perspective of national and EU environmental policies.