Ensuring effective use of evidence-based practice (EBP) for autism in schools is imperative due to the significantly increasing number of autistic students receiving school services each year. High-quality EBP use has proven challenging in schools. Research indicates implementation climate, or how EBP are supported, rewarded, and valued, and EBP resources are related to successful implementation. However, limited understanding of system-level contextual factors that impact EBP implementation for school-based providers makes development of appropriate implementation supports challenging. Understanding these factors is crucial for selecting and tailoring implementation strategies to support EBP scale up. In this observational study, California school-based providers (n = 1084) completed surveys related to implementation climate, leadership, autism experience and EBP implementation (use, competence, knowledge). Student outcomes included state level academic and behavioral indicators. Using an implementation science framework (Aarons et al., in Administration and Policy in Mental Health and Mental Health Services Research 38:4–23, 2011) and multilevel modeling, we examined the relationship between EBP Implementation and student outcomes and the moderation effects of provider and district level factors. Higher implementation climate predicted better EBP implementation outcomes, and proved more impactful when provider hands-on autism experience was low. Greater EBP resources predicted a higher percentage of students who met math standards only when district poverty level was high. Our findings suggested moderating effects on EBP implementation from both provider and system level factors. Implementation climate and resources may be especially key in addressing equity issues related to high poverty schools in which teachers often have less autism experience.