Web-based tools, for example, Google Forms, are readily available to develop online instruments to diagnose students’ understanding of chemistry topics. Multiple-tier multiple choice diagnostic instruments are easily developed using Google Forms, as well as easily administered to students. In addition, the results are automatically generated and can be downloaded as MS Excel files for further analysis. This paper describes the development and administration of a three-tier multiple choice web-based diagnostic instrument on chemical bonding based on a pen-and-paper version developed in a previous study, and the affordances of the web-based version over the pen-and-paper version. Students would need to choose an answer to the question stem in the first tier and support their answer by selecting reason(s) displayed in the second tier. The web-based version allows specific sets of second-tier options to be offered to students based on the first-tier answers chosen, the option to choose one or more second-tier reason(s) or supply their own reason(s), and to indicate their confidence in the answer-reason combinations selected. If the student has more than one conception for a given concept and is confident of them, then allowing the student to choose more than one reason can enable him/her to display all the relevant conceptions he/she has. These reasons can be tracked across related items instead of only one reason per item, possibly addressing the apparent lack of consistency of students’ use of specific conceptions across similar items reported in previous studies using diagnostic instruments. It also enables direct evidence of students’ possible multiple conceptions to be obtained, for example, when students confidently select the correct answer, correct reason, and/or incorrect reason(s), or incorrect answer and more than one reason in an item. Thus, this paper makes a strong argument for the use of such web-based instruments in the formative assessment of students’ understanding of chemistry. The instruments can also be made available to all teachers and students searching for such tools on the internet, allowing easy dissemination of research-based tools beyond the educational system in which the tools were developed to benefit teachers and students all around the world.