diff --git a/src/bootstrap/compile.rs b/src/bootstrap/compile.rs
index c56114f14caa9..99421a65a7e1d 100644
--- a/src/bootstrap/compile.rs
+++ b/src/bootstrap/compile.rs
@@ -838,12 +838,12 @@ pub fn run_cargo(
     let mut deps = Vec::new();
     let mut toplevel = Vec::new();
     let ok = stream_cargo(builder, cargo, tail_args, &mut |msg| {
-        let (filenames, crate_types) = match msg {
+        let (filenames, crate_types, kind, name) = match msg {
             CargoMessage::CompilerArtifact {
                 filenames,
-                target: CargoTarget { crate_types },
+                target: CargoTarget { crate_types, kind, name },
                 ..
-            } => (filenames, crate_types),
+            } => (filenames, crate_types, kind, name),
             _ => return,
         };
         for filename in filenames {
@@ -859,12 +859,24 @@ pub fn run_cargo(
 
             let filename = Path::new(&*filename);
 
-            // If this was an output file in the "host dir" we don't actually
-            // worry about it, it's not relevant for us
+            // If this was an output file in the "host dir", we want
+            // to ignore it if it's a build script.
             if filename.starts_with(&host_root_dir) {
-                // Unless it's a proc macro used in the compiler
                 if crate_types.iter().any(|t| t == "proc-macro") {
-                    deps.push((filename.to_path_buf(), true));
+                    deps.push((filename.to_path_buf(), /* host_dep */ true));
+                }
+
+                let is_build_script = kind == &["custom_build"]
+                    && crate_types == &["bin"]
+                    && name == "build-script-build";
+                // We don't care about build scripts, but we *do* care about proc-macro
+                // dependencies - the compiler needs their metadata when loading proc-macro
+                // crates. Anything that's not a build script should be a proc-macro dependency.
+                //
+                // FIXME: Have Cargo explicitly indicate build-script vs proc-macro dependencies,
+                // instead of relying on this check.
+                if !is_build_script {
+                    deps.push((filename.to_path_buf(), /* host_dep */ true));
                 }
                 continue;
             }
@@ -933,8 +945,8 @@ pub fn run_cargo(
     deps.extend(additional_target_deps.into_iter().map(|d| (d, false)));
     deps.sort();
     let mut new_contents = Vec::new();
-    for (dep, proc_macro) in deps.iter() {
-        new_contents.extend(if *proc_macro { b"h" } else { b"t" });
+    for (dep, host_dep) in deps.iter() {
+        new_contents.extend(if *host_dep { b"h" } else { b"t" });
         new_contents.extend(dep.to_str().unwrap().as_bytes());
         new_contents.extend(b"\0");
     }
@@ -1003,6 +1015,8 @@ pub fn stream_cargo(
 #[derive(Deserialize)]
 pub struct CargoTarget<'a> {
     crate_types: Vec<Cow<'a, str>>,
+    kind: Vec<Cow<'a, str>>,
+    name: Cow<'a, str>,
 }
 
 #[derive(Deserialize)]
diff --git a/src/librustc_metadata/creader.rs b/src/librustc_metadata/creader.rs
index a9e7a9f35dc36..1fd9762a4eae1 100644
--- a/src/librustc_metadata/creader.rs
+++ b/src/librustc_metadata/creader.rs
@@ -558,9 +558,10 @@ impl<'a> CrateLoader<'a> {
         dep_kind: DepKind,
     ) -> CrateNumMap {
         debug!("resolving deps of external crate");
-        if crate_root.is_proc_macro_crate() {
-            return CrateNumMap::new();
-        }
+
+        // Note that we need to resolve deps for proc-macro crates (just like normal crates)
+        // since we may need to decode `Span`s that reference the `CrateNums`
+        // of transitive dependencies
 
         // The map from crate numbers in the crate we're resolving to local crate numbers.
         // We map 0 and all other holes in the map to our parent crate. The "additional"
diff --git a/src/test/run-make-fulldeps/sysroot-crates-are-unstable/test.py b/src/test/run-make-fulldeps/sysroot-crates-are-unstable/test.py
index 927edff4c22a5..d9b883856c231 100644
--- a/src/test/run-make-fulldeps/sysroot-crates-are-unstable/test.py
+++ b/src/test/run-make-fulldeps/sysroot-crates-are-unstable/test.py
@@ -11,6 +11,10 @@
                  'rsbegin.o', 'rsend.o', 'dllcrt2.o', 'crt2.o', 'clang_rt']
 
 
+# This is a whitelist of crates which give an "compiled by an incompatible version of rustc"
+# error, due to being copied into the sysroot as proc-macro deps. See #69976
+INCOMPATIBLE_VER_CRATES = ['autocfg', 'cc']
+
 def convert_to_string(s):
     if s.__class__.__name__ == 'bytes':
         return s.decode('utf-8')
@@ -34,6 +38,11 @@ def check_lib(lib):
     stdout, stderr = exec_command([os.environ['RUSTC'], '-', '--crate-type', 'rlib',
                                    '--extern', '{}={}'.format(lib['name'], lib['path'])],
                                   to_input=('extern crate {};'.format(lib['name'])).encode('utf-8'))
+
+    if 'compiled by an incompatible version of rustc' in '{}{}'.format(stdout, stderr):
+        if lib['name'] in INCOMPATIBLE_VER_CRATES:
+            return True
+
     if not 'use of unstable library feature' in '{}{}'.format(stdout, stderr):
         print('crate {} "{}" is not unstable'.format(lib['name'], lib['path']))
         print('{}{}'.format(stdout, stderr))