To help students who traditionally underperform in general chemistry, we created a supplementary instruction (SI) course and called it the STEM-Dawgs Workshops. These workshops are an extension of the Peer-led Team Learning (PLTL) SI. In addition to peer-facilitated problem-solving, we incorporated two components inspired by learning sciences: (1) training in research-based study skills, and (2) evidence-based interventions targeting psychological and emotional support. Here we use an explanatory mixed methods approach to measure the impact of the STEM-Dawgs Workshops, with a focus on four sub-populations that are historically underrepresented in Chemistry: underrepresented minorities, females, low-income students, and first-generation students. Specifically, we compared three groups of students in the same General Chemistry course: students in general chemistry and not the workshops (“Gen Chem students”), students in the workshops (“STEM-Dawgs”), and students who volunteered for the workshops but did not get in (“Volunteers”). We tested hypotheses with regression models and conducted a series of focus group interviews with STEM-Dawgs. Compared to the Gen Chem population, the STEM-Dawg and Volunteer populations were enriched with students in all four under-represented sub-populations. Compared to Volunteers, STEM-Dawgs had increased exam scores, sense of belonging, perception of relevance, self-efficacy, and emotional satisfaction about chemistry. URM STEM-Dawgs had lower failure rates, and exam score achievement gaps that impacted first-generation and female Gen Chem students were eliminated in the STEM-Dawg population. Finally, female STEM-Dawgs had an increased sense of belonging and higher emotional satisfaction about chemistry than women Volunteers. Focus groups suggested that successes came in part from the supportive peer-learning environment and the relationships with peer facilitators. Together, our results indicate that this supplementary instruction model can raise achievement and improve affect for students who are underrepresented in chemistry.