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Traditional invariance testing via multiple group CFA is of limited utility when the number of groups is not small. The alignment method was recently developed for invariance testing when the number of groups is large. This study presents a unique application of the alignment method to test for invariance of several self-efficacy scales between intersectional groupings (ethnicity, gender, SES, and first-generation college attendance status) and longitudinally across two cohorts. This resulted in 48 groups. The results show that the English, control, and science self-efficacy scales are invariant across gender, SES, first-generation, and ethnicity. In addition, the math-specific self-efficacy scale has invariant factor loadings. However, one item has noninvariant intercepts when compared across studies, gender, SES, first-generation, and ethnicity groups.