Non-response in prevention programs for cardiometabolic diseases (CMD) in primary care is often overlooked. The aim for this study was to define factors that influence the primary response to a selective CMD prevention program and to determine response-enhancing strategies that influence the willingness to participate. We conducted a non-response analysis within a randomized controlled trial evaluating a selective CMD prevention program, the study was conducted from 2013 to 2018 in Netherlands. A random sample of 5616 patients from 15 general practices were invited to complete a risk score (RS) as initial step of the program. Non-responders received an additional questionnaire. The response on the risk score was 51% (n = 2872). From the 3558 non-response questionnaires sent, 786 (22%) were returned. In a multivariable multilevel regression analysis smoking was independently associated with non-response. Of all reported reasons for non-response ‘forgot/no time’ accounted for 45%. In total, 73% of the non-responders indicated to reconsider participation when approached differently. A personal approach by the patients’ own GP, using advertisements and informative campaigns are potentially the best methods to enhance the response. Although a relatively high proportion did not respond to the invitation for the risk score, the majority of them indicated to be willing to participate if a different invitation strategy would be used. With more time and energy, response rates for CMD prevention programs could possibly increase substantially. A next logical step in this process is to test potential response enhancing strategies in research setting.