Increasing connections and influences from near to far have changed social structures, access to natural resources, and essential livelihoods of smallholders (i.e., those with incomes generated primarily from natural resources on small rural properties). However, the potential benefits and negative impacts from these connections to smallholders’ livelihoods and social-ecological effects remain understudied. In this paper, we applied the frameworks of pericoupling and telecoupling (human-nature interactions between adjacent and distant systems, respectively) to systematically investigate how the flows linking smallholder systems to other systems affect their livelihoods, and causing varying economic, social, and environmental effects from case to case. We synthesized 12 cases of smallholder systems around the world that are linked to adjacent and distant systems through flows of goods, people, resources, and/or information. In each case, we summarized smallholders’ agency, i.e., capability on the formation or operation of these flows, and the changes on livelihoods on the economic, social, and environment effects. Results suggest that strong smallholder agency is associated more with positive than negative effects. Smallholders with medium to high agency have greater overall well-being within the area of interest. Smallholders integrated in pericoupled systems often have strong agency. Being spillover systems in an intercoupled system (e.g., large-scale agricultural investments) can often cause negative outcomes unless smallholders have additional pericoupling flows. Our findings suggest one potential approach to ending poverty and increasing well-being for smallholders is creating and increasing pericoupling flows to empower smallholders for desired livelihood and social-ecological outcomes.