Climate change heavily impacts smallholder farming worldwide. Cross-scale vulnerability assessment has a high potential to identify nested measures for reducing vulnerability of smallholder farmers. Despite their high practical value, there are currently only limited examples of cross-scale assessments. The presented study aims at assessing the vulnerability of smallholder farmers in the Northeast of Brazil across three scales: regional, farm and field scale. In doing so, it builds on existing vulnerability indices and compares results between indices at the same scale and across scales. In total, six independent indices are tested, two at each scale. The calculated indices include social, economic and ecological indicators, based on municipal statistics, meteorological data, farm interviews and soil analyses. Subsequently, indices and overlapping indicators are normalized for intra- and cross-scale comparison. The results show considerable differences between indices across and within scales. They indicate different activities to reduce vulnerability of smallholder farmers. Major shortcomings arise from the conceptual differences between the indices. We therefore recommend the development of hierarchical indices, which are adapted to local conditions and contain more overlapping indicators for a better understanding of the nested vulnerabilities of smallholder farmers.