COVID-19 has impacted the ecotourism industry significantly. It is imperative to examine and identify the key challenges in running rural ecotourism businesses to comprehend the mindset of the working community members before re-establishing a business model during endemic phase. This study aimed to explore and identify the resources and capabilities challenges perceived by the members of community-based ecotourism located in Marakau Village, Sabah. The study, which took place in 2021, employed a qualitative method through interviews among 10 key members of the Tagal Marakau Association responsible for a tagal ecotourism business. The interview was recorded and transcribed to identify common themes of issues. There was a total of 15 emerging issues: lack of capital, lack of business know-how, shortage of hospitality skills, lack of social capital, poor marketing ability, land dispute, absence of a strategic business model, poor financial planning, poor implementation of human resource practices, inadequate infrastructures, limited customer experiences, high fish habitat maintenance, external competitors, stakeholders support, and liability as a small business venture. These issues collated into five themes of business mindset domains: knowledge, attitude, skills, aspiration, and finance (KASA-F). Identifying the perceived challenges would help to understand the mindset of working rural community members to assist in re-formulating strategic plans for business sustainability in the post-COVID era.