The ecosystem-based adaptation (EbA) strategy is considered an effective approach to address the impact of climate change while ensuring the continued provision of ecosystem services on which farming depends. However, understanding the EbA’s effectiveness for smallholder farmers in the Savannah region remains limited. The focus of this study is to explore the EbA practices that have been implemented by farming communities in the Savannah region of Togo. The study aims to evaluate the effectiveness of these practices and the perceived co-benefits reported by 425 smallholder farmers who participated in the survey. Our findings show that five practices, namely agroforestry, crop rotation, grass hedge/stone bunds, in-field water drainage channel, and intercropping, were practiced mainly by smallholder farmers and perceived as effective in reducing their vulnerability to climate risks. In addition, the benefits observed were linked to all five EbA practices. As a result, we can determine the suitable combination of EbA practices that fulfil the requirements of smallholder farmers, including co-benefits such as food security, adaptation advantages, and ecosystem service provisions. Such findings provide insights for developing integrated agriculture and climate change policies suitable for weather-induced disaster-prone areas such as the Savannah region.