Consumption of poor-quality diets was noted as prevalent in the Lake Victoria Region, Kenya. As a strategy to communicate desirable change and promote healthy eating in the region, a 30-member panel of policymakers and implementers developed and proposed 12 food-based dietary guidelines (FBDGs) in 2017-2018. The objective of this study was to assess barriers in adopting the proposed FBDGs amongst community members in the lowlands of Kisumu and Homa Bay counties. Qualitative, descriptive cross-sectional design was used to collect data from 72 focus-group discussions (FGD). The FGD was conducted among 216 school going children (10-13y), 216 high school students (15-18y), 207 adult males (26-74y) and 211 females (18-71y). The participants were asked to state whether the proposed FBDGs reflected their daily dietary practices? If the answer was no, the FGD participants were asked to elaborate on the perceived barriers. Each FGD consisted of 8-12 participants. The demographics of FGD participants were collected before the start of FGD sessions. All FGD proceedings were audio-recorded and transcribed verbatim. Demographic information of participants was analyzed and presented using descriptive statistics. The FGD responses were coded and analyzed based on the main code, the barriers. Barriers to healthy eating in the study area were mainly linked to low production of food, food unavailability and inaccessibility. Specific factors which contributed to the food insecurity situation included; dry and sunny weather, seasonality in food availability, limited resources to secure potential farmland with fences, gender influence on land use, high cost of food, lack of money to purchase food, low income, sale of farm produce with resultant inadequate quantities of food consumed and inappropriate meal composition. Food insecurity was a perceived barrier to healthy eating in the lowlands of the Lake Victoria region. This research suggests the need to address food systems and economic structures to improve food production, distribution, accessibility and consumption in the region. Coding was done with the aid of NVivo8 (QSR International Pty Ltd Version 8, 2008). This study was registered with the Kenyan National Commission for Science Technology and Innovation (NACOSTI/P/18/12634/22291).