Traditionally, rice agroecosystems with complex wetland and dryland habitats have a great wealth of biological and cultural diversity. After the Green Revolution, rice production underwent a dramatic transformation driven by the expansion of monoculture rice fields, high-intensity cropping cycles, and utilization of commercial rice varieties and agrochemicals. The resulting loss of biocultural diversity has amplified an urgent call for another transformation to restore agrobiodiversity. Despite numerous interventions for knowledge dissemination on agrobiodiversity, little is known about the long-term impacts of those interventions on farmers’ practices and perceptions. Focusing on farm income and farmers’ perceptions towards rice farming systems, we report on findings from exploratory surveys conducted 5 years after a Farmer Field School (FFS) intervention that set up complex rice system (CRS) demonstration farms in Lamongan, Indonesia. Findings showed that the highest income was achieved by farmers who cultivated more than two species on their rice bunds, followed by farmers who grew two species, with the least income achieved by farmers who grew only rice. This study also demonstrated that proper selection of crops complementary to rice was a key to success, along with a slight widening of the rice bunds. Focus group discussions with three groups of farmers suggested that inputs and income were the most emphasized components of monoculture, while planting vegetables and other crops on rice bunds was an additional central component in rice farming systems with two and more than two species. These findings support the argument that diversifying rice fields could improve a rice farm’s economic performance. Therefore, incorporating economic considerations into the promotion of agrobiodiversity is critical to protect and sustain rice farming businesses.