'Personal Nutrition Management Tool' (PENUMAT) is an interactive web-based application which aims to help individuals seeking nutrition information on the Internet. However, little is known about the usability of such applications. The purpose of this study was to evaluate the usability of PENUMAT using multi-method approach. For an in-depth usability analysis, using a multi-method approach involving protocol analysis, interviews and a system usability scale (SUS) was adopted. The sample consisted of 10 healthy (five males and five females) volunteers between the ages of 22 and 60. The overall usability score was calculated; usability problems and users' opinions were obtained. All usability problems were classified according to the heuristics and listed with their frequencies. Overall, the usability score ranged from 77.5 to 100, with a median of 88.7. In-depth usability analysis exposed several usability problems mostly related to content, navigation and interactivity. Interview results showed that 'being personal and private' (70%) and 'providing personal feedbacks' (60%) were the most appreciated characteristics of the tool. Although the tool has an acceptable overall usability score, several unnoticed usability problems of the interface design were realised with the in-depth analysis. Therefore, the importance of using a multi-method analysis of usability was pointed out.