Coffee represents an important trade asset internationally. Around 70% of global coffee production is provided by 25 million smallholders farmers. In recent decades, coffee systems have been transformed into more intensified systems of coffee monoculture. The general objectives of this paper are to provide a better picture of the traditional coffee cropping systems and postharvest processes on-farm and to assess the environmental impacts, integrating the diversity of smallholder cropping systems. A Life Cycle Assessment from cradle to farm gate was performed for three cropping systems representative of Colombian coffee cultivation according to the associated crops and shadow trees: coffee alone (CA), coffee with transition shade (CTS), and coffee with permanent shade (CPS). The system studied includes inputs, agricultural production and postharvest operations using the wet method. The final product of farms is parchment bean coffee at farm gate. The technology used is representative of the average practices of smallholder coffee growers in the region. To address multiple functions of coffee, three functional units (FU) were selected: area by time (ha*year−1 unit area), productivity (ton of parchment coffee) and farmers income (1000 USD$). Seven midpoint categories were selected: climate change, acidification, terrestrial eutrophication, freshwater eutrophication, marine eutrophication, freshwater ecotoxicity, and water resource depletion. We present the life cycle inventory and impact assessment results from three types of cropping systems CA, CTS and CPS. For all FU, the CPS system has the lowest potential impact, excepted for marine eutrophication. CPS also has the highest coffee yields, however it has also the highest costs. Even if cropping system diversification is only one of multiple factors that influence environmental performance, agroforestry seems to be a promising path to reduce and mitigate environmental impacts by decreasing off-fam contributions (input fabrication). Results show the possibility that diversified cropping systems have an influence when assessing potential environmental impacts of coffee at farm gate and differences found might be influenced by shading in traditional coffee systems. Future work is needed to consider the real potential of CTS cropping system including land use and carbon dynamics. Assessments including social indicators and the rest of the value chain in particular coffee industrial transformation and utilization are also needed since the consumption stages are also a key driver to reduce the environmental footprint of coffee.