OrgoPrep, a summer preparatory program integrating multiple active-learning elements (i.e., interactive videos with problem-solving and feedback, synchronous peer-led instruction, and collaborative work), was previously shown to improve academic outcomes in organic chemistry for all students. The present study examined how OrgoPrep differentially impacted students belonging to historically marginalized groups, including those identifying as women, Black, Hispanic, or first-generation as well as those classified as low-income. As a result of multifaceted systemic barriers, these students receive lower grades and leave STEM at higher rates compared to their peers, highlighting the need for equity-focused educational interventions. Drawing upon Quantitative Critical Race Theory, educational debts in organic chemistry owed by society were calculated for each marginalized group. As a result of participating in OrgoPrep, educational debts in GPA points were reduced or mitigated for nearly all marginalized groups, with the largest benefits seen in Black students. Disproportionately larger mitigative impacts on attrition-measured via drop, failure, and withdrawal (DFW) rates-were detected for nearly all marginalized groups. Specifically, debts in the DFW rate were reduced for women and low-income students and eliminated for Black and Hispanic students. These findings demonstrate that OrgoPrep can appreciably reduce educational debts due to racism and sexism with a mixed impact on debts due to classism. Similar supplementary programs may play a key role in mitigating the effects of racism, sexism, and classism in the STEM pipeline.