Despite the risk of buying dangerous unregistered or counterfeit health supplement products online, the purchases still persist. This study aimed to identify the current preferred purchasing method and factors that influenced the preference. A cross-sectional study using simple random sampling was conducted among supplement purchasers within government servants in Putrajaya, Malaysia. Data were collected using an online self-reported questionnaire from 1st February to 1st August 2020. The traditional method became the preferred way of purchasing supplements (Traditional=68% vs Online=32%). However, younger and middle group (OR = 2.13, 95% CI = 1.41–3.21 and OR = 2.16, 95% CI = 1.22–3.82, respectively), females (OR = 1.38, 95% CI = 1.05–1.80) and, non-Malays (Indian and others, OR = 0.33, 95% CI = 0.11–0.95 and OR = 0.38, 95% CI = 0.17–0.88, respectively) significantly preferred online purchases. Product quality was the most important factor for both purchasing methods (P<0.001). Meanwhile, the main motivating factor for choosing the traditional method was ‘ease of getting the product to advise and relevant information (n=595, 72.4%), in online, it was ‘being able to read the product reviews through the internet (IT)’ (n=205, 52.8%). The majority of respondents checked for many similar supplement products before purchase (50.9% Traditional and 38.4% Online). Surprisingly, no significant differences were found in knowledge for identifying registered products between both methods (p=0.330). The traditional method was still preferred and indicates that the health awareness of the respondents is encouraging. However, this result cannot be generalized to the population. Hence, efforts to enhance public knowledge, awareness, and promoting the safety and efficacious issues on registered supplement products must be continued.