The Colombian Caribbean, one of the most biodiverse regions in the world, is facing great challenges in biodiversity conservation due to accelerated ecosystem transformations and the territorial planning required for peacemaking. We conducted a systematic review of 470 documents published between 1990 and 2015 to evaluate the progress of biodiversity and ecosystem services knowledge, identify biases, and define the priorities for research. Specifically, we describe the main characteristics of biodiversity studies, including the geographic distribution and the ecosystem services studied. We found limited participation by the social and interdisciplinary sciences. Researchers have focused mainly on taxonomic groups such as insects, birds, and mammals, ecosystems such as the tropical dry forest and regulating services. Some geographic areas have very few studies, corresponding to places affected by armed conflict. We propose that it is necessary to focus on plant and microorganism studies and those at the genetic and landscape level, as well as on less studied ecosystems such as urban and agro-ecosystems and places involved in armed conflict that have not been studied. We conclude by exposing insights to enhance some of the biases found and face the challenges: in the short term, the establishment of protected areas to guarantee the supply of ecosystem services for human well-being, in the middle term, an integrated territorial planning, and in the long term, the promotion of the social-ecological systems perspective. Ecosystem services concept reveals the link between biodiversity and human well-being and thus could have the potential to contribute to biodiversity conservation and peace construction in the Caribbean.