Chemistry courses tend to be challenging to teachers due to the increasing demotivation of students over STEM fields, which has increased lately due to online classes derived from the COVID-19 pandemic. Several didactic strategies have been applied to enhance their motivation, among which gamification has recently gained great attention. Although this methodology has been demonstrated to be very effective in diverse educational contexts, it requires considerable time and effort to be successful and enjoyable. To ease gamification’s implementation in higher education courses, we developed a customizable web platform named Fred! (Friendly Education). This Web site supports the pupils in self-managing their work and monitoring their progress to improve their academic performance. It also motivates them using a series of stimuli such as short-, medium-, and long-term bonuses, badges, tickets, and reminders. The web page was employed in General and Organic Chemistry subjects at a university in Mexico during the second term of 2021. To evaluate the proposal, a validated questionnaire using Keller’s ARCS model to measure motivation and adapted to this research was applied to 286 engineering undergraduates. The analysis consisted of the following sequence: examining data quality, matching groups, and group difference (experimental and control: EXP and CONTR) with a robust test. The matched groups (n = 61 in EXP and CONTR) were contrasted, and a large, standardized difference was found in motivation score and less dispersion in the EXP group.