Indonesia’s batik industry is growing rapidly, including the segment specializing in natural dyes. However, this has produced concerns regarding sustainability deriving from, for example, the use of environmental pollutants in the field. This research aims to propose a set of preliminary indicators to facilitate the assessment of the sustainability of the natural-dye-based batik industry. We selected Batik Preketek, a company in Pekalongan City, Indonesia, as a case study and received support from representative panellists who were knowledgeable on these issues. We employed a mixed-methods approach, with data collected from field observations, laboratory analyses, structured and semi-structured interviews and secondary sources. The validated indicators were then applied to assess the current sustainability of batik production. The indicators used included five indicators from the environmental dimension, four from the economic dimension and six from the social dimension. Assessment of the company’s sustainability level produced a score of 77.50, indicating that it could be categorized as sustainable. The instrument developed was proved capable of capturing major sustainability issues and delivering prioritized strategies to improve sustainability.