Makawanpur district in Central Nepal is recognized as a rich biodiversity hotspot, home to numerous indigenous underutilized fruit and nut species vital for the nutrition and income of rural households. Despite their importance, many of these species face threats from deforestation, agricultural expansion, and over-exploitation. Promoting the cultivation and domestication of these plants can aid in their conservation through sustainable use; however, limited funding necessitates prioritizing species for development. This study aimed to document indigenous fruit and nut species and their associated traditional knowledge to support species prioritization efforts. Surveys were conducted across three agro-climatic zones (400–2300 m a.s.l.) in natural forests, homegardens, farmers’ fields, and roadsides. Data on local names, uses, seasonal availability, and preference rankings were collected through field observations, interviews, and participatory rural appraisals involving key informants from four ethnic groups: Tamang, Bankaria, Chhetri, and Newar. A total of 54 indigenous fruit and nut species were identified, with 16 species cultivated in homegardens and only 7 partially domesticated. Sixteen species had market value for income generation. The knowledge of species utility varied among ethnic groups; Newar respondents, living in urban areas, identified 27 useful species, whereas Tamang, residing near forests, recognized 48. Seasonal availability fluctuated markedly, with only 1-2 species producing fruit from January to April, compared to 20 species in November. Therefore, priority setting for domestication should incorporate seasonality to ensure year-round fruit and nut supply and favor species widely used by multiple ethnic groups. Additional criteria include nutritional value, climate adaptability, and market potential to enhance conservation and livelihood benefits.