The coffee sector is estimated to have a retail market value in excess of USD 83 billion, and over 125 million jobs have been created in the global coffee chain. The coffee specialty market has recently increased significantly, generating opportunities to certify coffee beans produced by sustainable practices. This avoids practices potentially harmful to the environment. Agroforestry, organic farming, intercropping, and soil conservation strategies are examples of sustainable alternatives in the production of coffee. In this review, we focus on practices for the sustainable management of coffee plantations that can help farmers fight problems caused by global warming. More specifically, we address soil organic matter and microbiota, the use of Urochloa grass as intercrop in coffee plantations, shading systems (including agroforestry), and organic coffee production. We concluded that from the agronomic viewpoint, we already have production techniques that can replace traditional ones with significant advantages accruing to the quality of coffee orchard ecosystems. Nevertheless, we need scientific research efforts to deal with the existing gaps and the engagement of the whole coffee chain as a means of guaranteeing an adequate profit to those smallholders who adopt and maintain sustainable practice and are capable of bringing several positive changes to the coffee crop, including the use of microbia-based commercial products and new organic sources of nutrients to complement chemical fertilizers and improve coffee quality.