Instructional technology is growing at rapid rates. In the field of mathematics, virtual manipulatives are a research-based tool that has shown to have a positive impact on students' mathematic achievement, as well as student engagement in learning. In an effort to extend the research, this study investigated the impact of virtual manipulatives, when paired with research- (i.e., story-based math lessons) and evidence-based practices (i.e., systematic instruction, graphic organizers, manipulatives). This study used a single-case multiple probe across early numeracy math skills, with replication across student design. Two elementary students with autism and moderate intellectual disability used virtual manipulatives embedded within a story context to gain three early numeracy skills (i.e., set making, measurement, pattern making). Visual analysis of baseline, intervention, and maintenance phase data indicated a functional relationship between the use of virtual manipulatives and student math skills, and statistical analysis (Tau-U) further supported this with a large effect. Additionally, the virtual manipulatives were found to be more engaging than the tangible math manipulatives. Students were able to generalize and maintain the early numeracy skills across new math contexts. Implications and recommendations for practice and future research are provided.