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Objective: We investigated cross-level effects, which are concurrent changes across neural and cognitive-behavioral levels of analysis as teams interact, between neurophysiology and team communication variables under variations in team training. Background: When people work together as a team, they develop neural, cognitive, and behavioral patterns that they would not develop individually. It is currently unknown whether these patterns are associated with each other in the form of cross-level effects. Method: Team-level neurophysiology and latent semantic analysis communication data were collected from submarine teams in a training simulation. We analyzed whether (a) both neural and communication variables change together in response to changes in training segments (briefing, scenario, or debriefing), (b) neural and communication variables mutually discriminate teams of different experience levels, and (c) peak cross-correlations between neural and communication variables identify how the levels are linked. Results: Changes in training segment led to changes in both neural and communication variables, neural and communication variables mutually discriminated between teams of different experience levels, and peak cross-correlations indicated that changes in communication precede changes in neural patterns in more experienced teams. Conclusion: Cross-level effects suggest that teamwork is not reducible to a fundamental level of analysis and that training effects are spread out across neural and cognitive-behavioral levels of analysis. Cross-level effects are important to consider for theories of team performance and practical aspects of team training. Application: Cross-level effects suggest that measurements could be taken at one level (e.g., neural) to assess team experience (or skill) on another level (e.g., cognitive-behavioral).