diff --git a/compiler/rustc_driver_impl/src/lib.rs b/compiler/rustc_driver_impl/src/lib.rs
index e56347ab38e..f38adefa7c0 100644
--- a/compiler/rustc_driver_impl/src/lib.rs
+++ b/compiler/rustc_driver_impl/src/lib.rs
@@ -162,9 +162,10 @@ pub fn abort_on_err<T>(result: Result<T, ErrorGuaranteed>, sess: &Session) -> T
 pub trait Callbacks {
     /// Called before creating the compiler instance
     fn config(&mut self, _config: &mut interface::Config) {}
-    /// Called after parsing. Return value instructs the compiler whether to
+    /// Called after parsing the crate root. Submodules are not yet parsed when
+    /// this callback is called. Return value instructs the compiler whether to
     /// continue the compilation afterwards (defaults to `Compilation::Continue`)
-    fn after_parsing<'tcx>(
+    fn after_crate_root_parsing<'tcx>(
         &mut self,
         _compiler: &interface::Compiler,
         _queries: &'tcx Queries<'tcx>,
@@ -184,7 +185,6 @@ pub trait Callbacks {
     /// continue the compilation afterwards (defaults to `Compilation::Continue`)
     fn after_analysis<'tcx>(
         &mut self,
-        _handler: &EarlyErrorHandler,
         _compiler: &interface::Compiler,
         _queries: &'tcx Queries<'tcx>,
     ) -> Compilation {
@@ -407,7 +407,7 @@ fn run_compiler(
                 return early_exit();
             }
 
-            if callbacks.after_parsing(compiler, queries) == Compilation::Stop {
+            if callbacks.after_crate_root_parsing(compiler, queries) == Compilation::Stop {
                 return early_exit();
             }
 
@@ -445,7 +445,7 @@ fn run_compiler(
 
             queries.global_ctxt()?.enter(|tcx| tcx.analysis(()))?;
 
-            if callbacks.after_analysis(&handler, compiler, queries) == Compilation::Stop {
+            if callbacks.after_analysis(compiler, queries) == Compilation::Stop {
                 return early_exit();
             }
 
diff --git a/compiler/rustc_interface/src/queries.rs b/compiler/rustc_interface/src/queries.rs
index 29a5837eb7c..449d7a29590 100644
--- a/compiler/rustc_interface/src/queries.rs
+++ b/compiler/rustc_interface/src/queries.rs
@@ -114,6 +114,7 @@ impl<'tcx> Queries<'tcx> {
             .compute(|| passes::parse(self.session()).map_err(|mut parse_error| parse_error.emit()))
     }
 
+    #[deprecated = "pre_configure may be made private in the future. If you need it please open an issue with your use case."]
     pub fn pre_configure(&self) -> Result<QueryResult<'_, (ast::Crate, ast::AttrVec)>> {
         self.pre_configure.compute(|| {
             let mut krate = self.parse()?.steal();
@@ -171,6 +172,7 @@ impl<'tcx> Queries<'tcx> {
     pub fn global_ctxt(&'tcx self) -> Result<QueryResult<'_, &'tcx GlobalCtxt<'tcx>>> {
         self.gcx.compute(|| {
             let sess = self.session();
+            #[allow(deprecated)]
             let (krate, pre_configured_attrs) = self.pre_configure()?.steal();
 
             // parse `#[crate_name]` even if `--crate-name` was passed, to make sure it matches.
diff --git a/compiler/rustc_smir/src/rustc_internal/mod.rs b/compiler/rustc_smir/src/rustc_internal/mod.rs
index 73b8e060dd8..4203990ab05 100644
--- a/compiler/rustc_smir/src/rustc_internal/mod.rs
+++ b/compiler/rustc_smir/src/rustc_internal/mod.rs
@@ -16,7 +16,6 @@ use rustc_driver::{Callbacks, Compilation, RunCompiler};
 use rustc_interface::{interface, Queries};
 use rustc_middle::mir::interpret::AllocId;
 use rustc_middle::ty::TyCtxt;
-use rustc_session::EarlyErrorHandler;
 pub use rustc_span::def_id::{CrateNum, DefId};
 
 fn with_tables<R>(mut f: impl FnMut(&mut Tables<'_>) -> R) -> R {
@@ -233,7 +232,6 @@ where
     /// continue the compilation afterwards (defaults to `Compilation::Continue`)
     fn after_analysis<'tcx>(
         &mut self,
-        _handler: &EarlyErrorHandler,
         _compiler: &interface::Compiler,
         queries: &'tcx Queries<'tcx>,
     ) -> Compilation {
diff --git a/src/tools/miri/src/bin/miri.rs b/src/tools/miri/src/bin/miri.rs
index 97718f1f4a9..1e9219d4bb2 100644
--- a/src/tools/miri/src/bin/miri.rs
+++ b/src/tools/miri/src/bin/miri.rs
@@ -59,7 +59,6 @@ impl rustc_driver::Callbacks for MiriCompilerCalls {
 
     fn after_analysis<'tcx>(
         &mut self,
-        handler: &EarlyErrorHandler,
         _: &rustc_interface::interface::Compiler,
         queries: &'tcx rustc_interface::Queries<'tcx>,
     ) -> Compilation {
@@ -68,7 +67,8 @@ impl rustc_driver::Callbacks for MiriCompilerCalls {
                 tcx.sess.fatal("miri cannot be run on programs that fail compilation");
             }
 
-            init_late_loggers(handler, tcx);
+            let handler = EarlyErrorHandler::new(tcx.sess.opts.error_format);
+            init_late_loggers(&handler, tcx);
             if !tcx.crate_types().contains(&CrateType::Executable) {
                 tcx.sess.fatal("miri only makes sense on bin crates");
             }
diff --git a/tests/run-make-fulldeps/obtain-borrowck/driver.rs b/tests/run-make-fulldeps/obtain-borrowck/driver.rs
index 04c551cf4bb..b59a65a713f 100644
--- a/tests/run-make-fulldeps/obtain-borrowck/driver.rs
+++ b/tests/run-make-fulldeps/obtain-borrowck/driver.rs
@@ -27,7 +27,7 @@ use rustc_interface::{Config, Queries};
 use rustc_middle::query::queries::mir_borrowck::ProvidedValue;
 use rustc_middle::query::{ExternProviders, Providers};
 use rustc_middle::ty::TyCtxt;
-use rustc_session::{Session, EarlyErrorHandler};
+use rustc_session::Session;
 use std::cell::RefCell;
 use std::collections::HashMap;
 use std::thread_local;
@@ -58,7 +58,6 @@ impl rustc_driver::Callbacks for CompilerCalls {
     // the result.
     fn after_analysis<'tcx>(
         &mut self,
-        _handler: &EarlyErrorHandler,
         compiler: &Compiler,
         queries: &'tcx Queries<'tcx>,
     ) -> Compilation {