Micro and small enterprises (MSEs) play a significant role in developing countries such as Ecuador. The food and beverage industry is essential for Ecuador’s economy, contributing approximately 5% to its GDP. Focusing on the impact of COVID-19 on the industry, this mixed research takes a qualitative and quantitative approach involving four stages: foundation, prefield, field, and reporting. The fieldwork was carried out when Ecuador’s economy reopened in September 2020, which saw demand increase gradually, production capacity recovering, mobility return to normal levels, and curfew restrictions reduced. As far as biosecurity protocols were concerned, communities were allowed to resume pre-pandemic activities, provided they complied with social distancing, permanent mask wearing, and strict cleaning procedures. The effect on each company’s process depends on the activities they adopted to mitigate the risk of the COVID-19 pandemic risk, e.g., service companies experienced, on average, a 22% cost increase due to the purchase of cleaning supplies, while manufacturing companies were more likely to have related measures in place and so the effect on them was on a comparatively smaller scale.