The sustainability of agriculture is questioned due to major negative environmental and socioeconomic impacts. To improve the state of agriculture, various management changes have been proposed. Different tools, with varying characteristics, sustainability framing and indicators, have been used to evaluate the impact of these changes on sustainability. Here, we review 119 tools for farm sustainability assessment and compare their use, sustainability dimensions, themes and types of indicators used for biodiversity conservation, farm viability and gender equity. Our main findings are that (1) tools could be classified into five groups that differ in stakeholder participation and model used for calculating sustainability, (2) seven different sustainability framings are used and (3) only two out of 29 indicators screened address impacts of farming system while the others address drivers, pressures or states of the system. The tools were grouped in “Long-term monitoring of farm activities” (11%), “Ex-ante assessment of sustainability with bioeconomic models” (9%), “Survey- and indicator-based assessment of tools” (41%), “Consultation-based assessment” (25%) and “Active engagement of stakeholder-based assessment” (14%). The “classical view of sustainability”, with the economic, social and environmental pillars, was used in 61% of the papers. Based on these findings, we suggest (1) development of temporal dynamic assessment of farm sustainability with active involvement of stakeholders in the framing of sustainability and design of indicators to achieve reliable and relevant assessment outcomes. We recommend (2) adoption of more complex sustainability framings dealing with emerging system properties, namely resilience, viability and stability. In these, (3) governance/institutional dimensions should be emphasised, and social themes targeting farmers’ characteristics should be included. Finally, (4) use of impact indicators in farm sustainability assessments is critical, and they should be designed to contribute to scientifically rigorous and relevant assessments of farming system sustainability.