diff --git a/src/cargo/core/compiler/custom_build.rs b/src/cargo/core/compiler/custom_build.rs
index 9d45ab41fc6..86f00a84dda 100644
--- a/src/cargo/core/compiler/custom_build.rs
+++ b/src/cargo/core/compiler/custom_build.rs
@@ -267,7 +267,12 @@ fn build_work(cx: &mut Context<'_, '_>, unit: &Unit) -> CargoResult<Job> {
             }
         })
         .collect::<Vec<_>>();
-    let crate_name = unit.target.crate_name();
+    let library_name = unit
+        .pkg
+        .targets()
+        .iter()
+        .find(|t| t.is_lib())
+        .map(|t| t.crate_name());
     let pkg_descr = unit.pkg.to_string();
     let build_script_outputs = Arc::clone(&cx.build_script_outputs);
     let id = unit.pkg.package_id();
@@ -277,7 +282,7 @@ fn build_work(cx: &mut Context<'_, '_>, unit: &Unit) -> CargoResult<Job> {
     let host_target_root = cx.files().host_dest().to_path_buf();
     let all = (
         id,
-        crate_name.clone(),
+        library_name.clone(),
         pkg_descr.clone(),
         Arc::clone(&build_script_outputs),
         output_file.clone(),
@@ -397,7 +402,7 @@ fn build_work(cx: &mut Context<'_, '_>, unit: &Unit) -> CargoResult<Job> {
         paths::write(&root_output_file, util::path2bytes(&script_out_dir)?)?;
         let parsed_output = BuildOutput::parse(
             &output.stdout,
-            crate_name,
+            library_name,
             &pkg_descr,
             &script_out_dir,
             &script_out_dir,
@@ -419,12 +424,12 @@ fn build_work(cx: &mut Context<'_, '_>, unit: &Unit) -> CargoResult<Job> {
     // itself to run when we actually end up just discarding what we calculated
     // above.
     let fresh = Work::new(move |state| {
-        let (id, crate_name, pkg_descr, build_script_outputs, output_file, script_out_dir) = all;
+        let (id, library_name, pkg_descr, build_script_outputs, output_file, script_out_dir) = all;
         let output = match prev_output {
             Some(output) => output,
             None => BuildOutput::parse_file(
                 &output_file,
-                crate_name,
+                library_name,
                 &pkg_descr,
                 &prev_script_out_dir,
                 &script_out_dir,
@@ -476,7 +481,7 @@ fn insert_warnings_in_build_outputs(
 impl BuildOutput {
     pub fn parse_file(
         path: &Path,
-        crate_name: String,
+        library_name: Option<String>,
         pkg_descr: &str,
         script_out_dir_when_generated: &Path,
         script_out_dir: &Path,
@@ -486,7 +491,7 @@ impl BuildOutput {
         let contents = paths::read_bytes(path)?;
         BuildOutput::parse(
             &contents,
-            crate_name,
+            library_name,
             pkg_descr,
             script_out_dir_when_generated,
             script_out_dir,
@@ -497,11 +502,11 @@ impl BuildOutput {
 
     // Parses the output of a script.
     // The `pkg_descr` is used for error messages.
-    // The `crate_name` is used for determining if RUSTC_BOOTSTRAP should be allowed.
+    // The `library_name` is used for determining if RUSTC_BOOTSTRAP should be allowed.
     pub fn parse(
         input: &[u8],
         // Takes String instead of InternedString so passing `unit.pkg.name()` will give a compile error.
-        crate_name: String,
+        library_name: Option<String>,
         pkg_descr: &str,
         script_out_dir_when_generated: &Path,
         script_out_dir: &Path,
@@ -590,12 +595,21 @@ impl BuildOutput {
                         // behavior, so still only give a warning.
                         // NOTE: cargo only allows nightly features on RUSTC_BOOTSTRAP=1, but we
                         // want setting any value of RUSTC_BOOTSTRAP to downgrade this to a warning
-                        // (so that `RUSTC_BOOTSTRAP=crate_name` will work)
-                        let rustc_bootstrap_allows = |name: &str| {
+                        // (so that `RUSTC_BOOTSTRAP=library_name` will work)
+                        let rustc_bootstrap_allows = |name: Option<&str>| {
+                            let name = match name {
+                                // as of 2021, no binaries on crates.io use RUSTC_BOOTSTRAP, so
+                                // fine-grained opt-outs aren't needed. end-users can always use
+                                // RUSTC_BOOTSTRAP=1 from the top-level if it's really a problem.
+                                None => return false,
+                                Some(n) => n,
+                            };
                             std::env::var("RUSTC_BOOTSTRAP")
                                 .map_or(false, |var| var.split(',').any(|s| s == name))
                         };
-                        if nightly_features_allowed || rustc_bootstrap_allows(&*crate_name) {
+                        if nightly_features_allowed
+                            || rustc_bootstrap_allows(library_name.as_deref())
+                        {
                             warnings.push(format!("Cannot set `RUSTC_BOOTSTRAP={}` from {}.\n\
                                 note: Crates cannot set `RUSTC_BOOTSTRAP` themselves, as doing so would subvert the stability guarantees of Rust for your project.",
                                 val, whence
@@ -608,7 +622,7 @@ impl BuildOutput {
                                 help: If you're sure you want to do this in your project, set the environment variable `RUSTC_BOOTSTRAP={}` before running cargo instead.",
                                 val,
                                 whence,
-                                crate_name,
+                                library_name.as_deref().unwrap_or("1"),
                             );
                         }
                     } else {
@@ -865,7 +879,11 @@ fn prev_build_output(cx: &mut Context<'_, '_>, unit: &Unit) -> (Option<BuildOutp
     (
         BuildOutput::parse_file(
             &output_file,
-            unit.target.crate_name(),
+            unit.pkg
+                .targets()
+                .iter()
+                .find(|t| t.is_lib())
+                .map(|t| t.crate_name()),
             &unit.pkg.to_string(),
             &prev_script_out_dir,
             &script_out_dir,
diff --git a/tests/testsuite/build_script_env.rs b/tests/testsuite/build_script_env.rs
index f3cb4475948..d4cb7ca2d7f 100644
--- a/tests/testsuite/build_script_env.rs
+++ b/tests/testsuite/build_script_env.rs
@@ -110,18 +110,17 @@ fn rerun_if_env_or_file_changes() {
 
 #[cargo_test]
 fn rustc_bootstrap() {
+    let build_rs = r#"
+        fn main() {
+            println!("cargo:rustc-env=RUSTC_BOOTSTRAP=1");
+        }
+    "#;
     let p = project()
         .file("Cargo.toml", &basic_manifest("has-dashes", "0.0.1"))
-        .file("src/main.rs", "fn main() {}")
-        .file(
-            "build.rs",
-            r#"
-            fn main() {
-                println!("cargo:rustc-env=RUSTC_BOOTSTRAP=1");
-            }
-        "#,
-        )
+        .file("src/lib.rs", "#![feature(rustc_attrs)]")
+        .file("build.rs", build_rs)
         .build();
+    // RUSTC_BOOTSTRAP unset on stable should error
     p.cargo("build")
         .with_stderr_contains("error: Cannot set `RUSTC_BOOTSTRAP=1` [..]")
         .with_stderr_contains(
@@ -129,16 +128,17 @@ fn rustc_bootstrap() {
         )
         .with_status(101)
         .run();
+    // RUSTC_BOOTSTRAP unset on nightly should warn
     p.cargo("build")
         .masquerade_as_nightly_cargo()
         .with_stderr_contains("warning: Cannot set `RUSTC_BOOTSTRAP=1` [..]")
         .run();
-    // RUSTC_BOOTSTRAP set to the name of the crate
+    // RUSTC_BOOTSTRAP set to the name of the library should warn
     p.cargo("build")
         .env("RUSTC_BOOTSTRAP", "has_dashes")
         .with_stderr_contains("warning: Cannot set `RUSTC_BOOTSTRAP=1` [..]")
         .run();
-    // RUSTC_BOOTSTRAP set to some random value
+    // RUSTC_BOOTSTRAP set to some random value should error
     p.cargo("build")
         .env("RUSTC_BOOTSTRAP", "bar")
         .with_stderr_contains("error: Cannot set `RUSTC_BOOTSTRAP=1` [..]")
@@ -147,4 +147,25 @@ fn rustc_bootstrap() {
         )
         .with_status(101)
         .run();
+
+    // Tests for binaries instead of libraries
+    let p = project()
+        .file("Cargo.toml", &basic_manifest("foo", "0.0.1"))
+        .file("src/main.rs", "#![feature(rustc_attrs)] fn main()")
+        .file("build.rs", build_rs)
+        .build();
+    // RUSTC_BOOTSTRAP unconditionally set when there's no library should warn
+    p.cargo("build")
+        .masquerade_as_nightly_cargo()
+        .with_stderr_contains("warning: Cannot set `RUSTC_BOOTSTRAP=1` [..]")
+        .run();
+    // RUSTC_BOOTSTRAP conditionally set when there's no library should error (regardless of the value)
+    p.cargo("build")
+        .env("RUSTC_BOOTSTRAP", "foo")
+        .with_stderr_contains("error: Cannot set `RUSTC_BOOTSTRAP=1` [..]")
+        .with_stderr_does_not_contain(
+            "help: [..] set the environment variable `RUSTC_BOOTSTRAP=1` [..]",
+        )
+        .with_status(101)
+        .run();
 }