Smallholder dairy farmers (SDF) in developing countries often have limited understanding on the importance of cow comfort. We conducted a randomized controlled trial with 124 cows on 114 Kenyan SDF to determine the status of cow comfort, to assess compliance to farm-specific cow comfort recommendations, and to evaluate the impacts of the farm-specific interventions on cow comfort. On the first farm visit, stall dimensions and characteristics (e.g. stall base hardness and hygiene) were measured and categorized as adequate, marginal or inadequate/absent based on cow size. Where measurements were not adequate, farm-specific cow comfort recommendations were provided in written and oral form to the randomly allocated intervention group of farms (n = 74). On the second farm visit two months later, the same measurements were taken, and percent compliance to the recommendations was evaluated. A discomfort index was arithmetically calculated based on the stall base hardness (scale was 1–3 for soft to hard) and hygiene (scale was 1–5 for clean to dirty). Multivariable linear regression models were used to determine specific associations with the discomfort index. On the first visit, the mean stall base hardness and stall hygiene scores were 1.7 and 2.3, respectively, for a mean discomfort index of 4.0. Intervention farmers were given 3.9 comfort recommendations, on average, and complied with 2.1 recommendations, significantly improving the discomfort index at visit two to 3.3. The overall compliance to the recommendations was 49.0%. In a final model, the interaction between intervention group and visit number was significantly associated with discomfort index, indicating that after adjusting for baseline discomfort indices, the intervention led to better cow comfort. Specifically, bedding type and neck rail positioning were significantly associated with discomfort index. We concluded that farmers can substantially improve cow comfort on SDF by providing recommendations to them. Farm advisors should include cow comfort recommendations to SDF.