(1) Background: Indigenous chickens (Gallus domesticus) (ICs) are an essential component of agriculture and rural livelihood among 80% of small-scale farmers (SSFs) in Sub-Saharan Africa (SSA). However, in the past decade, significant losses of Indigenous Chicken Animal Genetic Resources (ICAnGR) resulting from poultry diseases, imported exotic breeds, poor market access, and uncontrolled crossbreeding have been reported. This study aimed to investigate the status of IC-AnGR and assess the major challenges affecting the production of ICs. (2) Methods: We surveyed 358 households in eastern, central, and southern livelihood zones, comprising 81.6% males and 17.6% females. (3) Results: Our study shows that respondents owned 16,112 ICs, 3026 goats, and 5183 herds of cattle. Overall, 77.4% of chicken breeds were ICs and 22.6% were exotic. Across the three zones, 18–44% reported the introduction or adoption of exotic breeds in the past decade, with most households sourcing breeding stock from local communities and family and friends at 45% and 28.6%, respectively. Farmers gave various reasons for adopting new chicken breeds, including fast growth (21.7%), larger mature sizes (21.66%), and resistance to diseases at 15.2%. Overall, 92.5% of farmers agreed or strongly agreed that some IC breeds disappeared in the past decade and nearly 90% were concerned. Some attributed the loss to poultry diseases. (4) Conclusion: Deliberate policies to promote the sustainable use and conservation of ICs are critical in Zambia.