This study presents a designated Flipped Classroom (FC) mathematics environment that utilizes a unique online platform designed for Arab minority students in Israel. It investigates how studying in an FC affects conceptual understanding and motivation to study mathematics among Arab high school students. The study also explores the factors that contribute to effective learning in the FC environment. Participants were 75 Arab high school students in 10th and 11th grade who studied advanced mathematics. Each grade group was randomly divided into two subgroups: an FC group and a traditional classroom group (comparison group). Quantitative questionnaires given before and after the learning program served to measure students’ motivation and conceptual understanding of the derivative and integral topics. Additionally, a random sample of students who studied in the FC group and the teacher who taught all the groups were interviewed. The study describes the positive effect an FC environment has on students' conceptual understanding, particularly for 11th graders. The participants mostly appreciated how the FC resulted in less lecturing in class. The study contributes to the literature about FC among minorities and contributes to national and international efforts being made to reduce the gap in mathematics achievements between minorities and other sectors.