Sustainable energy systems based on efficiency, low-carbon, and smart technologies are essential for the future energy transition. A new integrated sustainability assessment framework (ISAF) is required to evaluate cross-cutting subjects and future research. Sustainability analysis based on conventional dimensions and complementary categories is needed for a digital energy transition. Industry 4.0 created a new platform and technological portfolio to improve the efficiency and automation of cleaner energy systems (lower environmental and social impacts and high performance). To address these aspects, a new methodology based on bibliometric analysis, systematic literature review, and energy systems thinking was developed. From Scopus and Web of Science databases, 1521 and 959 documents were respectively compiled and merged to select 181 articles related to these research subjects between 2017 and 2021. Out of this total, 62 articles from industrial manufacturing were identified as the most representative energy consumption sub-sector. These articles were analysed from the ISAF using conventional dimensions (environmental, economic, and social) and complementary categories of sustainability (technological innovation, governance and life cycle). The main findings reveal that worldwide studies addressing the nexus between Industry 4.0, Energy and Sustainability have increased significantly in recent years, primaly in high-income countries. These studies have centred on the industrial manufacturing subsector, assessing sustainability unevenly by focusing mainly on technological and environmental issues. Research gaps indicate that a comprehensive assessment of social, governance, and life cycle aspects is still required.