I'm having some issues with my setup where I have projects A depends on B, but because B gets loaded after A, it throws this error:

org.gradle.api.internal.plugins.PluginApplicationException: Failed to apply plugin 'org.jetbrains.kotlin.jvm'.
   ...
org.gradle.api.internal.DefaultMutationGuard$IllegalMutationException: Gradle#projectsEvaluated(Action) on build 'project_root_name' cannot be executed in the current context.
   ...

The dependency is added as

api(project(":B", "namedElements"))

as required by the toolchain. How would I go about fixing it?

Doesn't sound like it should be related to project dependencies. Can you provide an MCVE?