In many countries research evaluations confer high importance to mainstream journals, which are considered to publish excellent research. Accordingly, research evaluation policies discourage publications in other non-mainstream journals under the assumption that they publish low quality research. This approach has prompted a policy debate in low and middle-income countries, which face financial and linguistic barriers to access mainstream journals. A common criticism of the current evaluation practices is that they can hinder the development of certain topics that are not published in mainstream journals although some of them might be of high local relevance. In this article, we examine this issue by exploring the functions of non-mainstream journals in scientific communication. We interviewed researchers from agricultural sciences, business and management, and chemistry in Colombia on their reasons to publish in non-mainstream journals. We found that non-mainstream journals serve the following functions: 1) offer a space for initiation into publishing (training); 2) provide a link between articles in mainstream journals and articles read by communities with limited access to them (knowledge-bridging); 3) publish topics that are not well covered by mainstream journals (knowledge gap-filling). Therefore, publication in non-mainstream journals cannot be attributed only to ‘low scientific quality’ research. They also fulfil specific communication functions. These results suggest that research evaluation policy in low and middle-income countries should consider assigning greater value to non-mainstream journals given their role in bridging and disseminating potentially useful and novel knowledge.