Trade-offs in integrated natural resource management are both social and biophysical. AHI has worked in both areas, using both qualitative and quantitative methods. From a social standpoint, some individuals stand to gain and others to lose from current and alternative natural resource management scenarios. Selection of particular tree or livestock species, for example, has a profound impact on who benefits most from system innovations, given traditional domains of activity and customary property rights. In the eastern African highlands, for example, women generally have control over some tree and livestock products but often cannot own or dispose of the tree or animal. Efforts to plan more compatible tree species around springs, on the other hand, can be beneficial to women and children given their role in water collection but can be detrimental to women in disposing of an important source of fuel wood (i.e. Eucalyptus). A highly marketable variety of tomato introduced in Lushoto, Tanzania, stimulated profitable partnerships between youth and elders to combine complementary resources (land on the one hand, and labor and nutrient resources on the other), yet diverted limited nutrient resources from other farms.

Biophysical trade-offs are also abundant. Farmers' decisions on cropland allocation to different crops and enterprises has an important influence on diverse outcomes, often with strong trade-offs between income, human nutrition and soil fertility. If a crop variety is selected that maximizes the yield of grain, it is unlikely to yield much fodder for livestock—representing a clear trade-offs between crop and livestock components of the system. In a similar vein, if fast-growing tree species are favored for their growth rate and yield of timber, there are likely to be substantial repercussions for crops (who may compete with trees for sunlight, moisture and nutrients), livestock (who may not benefit from the trees if fodder quality is poor) and springs (as growth rates may be proportional to water consumption).

Within AHI, social trade-offs are being addressed primarily through multi-stakeholder negotiations, where gains and losses to different local groups are acknowledged openly and "socially optimal" solutions negotiated. This is illustrated in Ginchi benchmark site, where negotiations were carried out between the owner of land around a spring (whose Eucalyptus woodlot is the farmers' form of savings) and spring users. The interests and potential losses (in the form of income or water) to the different stakeholders were openly acknowledged, and a more optimal outcome identified—namely, removal of the woodlot in exchange for new seedlings donated by all spring users. Biophysical trade-offs are being assessed through more quantitative, systems modeling approaches. Trade-offs of diverse cropland allocation scenarios are being assessed, for example, in terms of gains and losses to household nutrition, income, risk and soil fertility. Potato researchers at Ginchi are also looking at the trade-offs associated with increased production of a nutrient-demanding crop (seed potato) in the area, in terms of nutrients diverted and income lost to other farm enterprises. This will enable farmers to understand from the outset the risks associated with innovation so that they can be better equipped to manage the system spin-offs as they strive to increase household incomes.