In order to identify sustainable management solutions for small-scale farmer agroecosystems, a better understanding of these dynamic forest–farmland systems, existing farming and forestry strategies, and farmer perspectives is important. We examined the relationship between agricultural land use patterns and farmers’ practices and identified existing and potential characteristics of healthy agroecosystems at local scale in the context of village communities in Zanzibar, Tanzania. With in-depth household survey and participatory mapping, five distinct cropping patterns were identified and their relation to land cover elucidated. Consequences of the diverse local farming strategies to field level cultivation patterns are dynamic. However, long-term adaptation of the local farmers to prevailing edaphic site conditions and resource-poor circumstances create fragmented but fairly stable land use patterns at landscape level. By integrating local expert knowledge and realities with scientific knowledge, we identified sustainable agroecosystem characteristics and farming practices, which are knowledge-intensive, alternative and adaptable to local conditions. Some of these practices are already a part of the local farming strategies and some require training and higher level support to reach healthier agroecosystem and better food security. They also offer potential opportunities for forest conservation since their tree-based nature provide forest products to the communities.