In agricultural production systems with shade trees, such as coffee, the increase in greenhouse gas (GHG) emissions from production intensification can be compensated for, or even outweighed, by the increase in carbon sequestration into above-ground and below-ground tree biomass. We use data from a long-term coffee agroforestry experiment in Costa Rica to evaluate the trade-offs between intensification, profitability and net greenhouse gas emissions through two scenarios. First, by assessing the GHG emissions associated with conversion from shaded to more profitable full-sun (un-shaded) systems, we calculate the break-even carbon price which would need to be paid to offset the opportunity cost of not converting. The price per tCO2e of emissions reduction required to compensate for the coffee production revenue foregone varies widely from 9.3 to 196.3 US$ amongst different shaded systems. Second, as an alternative to intensification, production area can be extended onto currently forested land. We estimate this land-use change required to compensate for the shortfall in profitability from retaining lower intensity coffee production systems. For four of the five shade types tested, this land-use change causes additional GHG emissions >5 tCO2e ha−1 yr−1 resulting in net emissions >8 tCO2e ha−1 yr−1 for the whole system. We conclude that instead, by intensifying production, mechanisms similar to REDD that are based on reducing emissions through avoided land-use change (REAL) could play a major role in increasing the climate change mitigation success of agroforestry systems at the same time as aiding REDD through reducing pressure for further forest conversion to agriculture.