diff --git a/compiler/rustc_codegen_ssa/src/back/link.rs b/compiler/rustc_codegen_ssa/src/back/link.rs
index 59447e9de1350..c9a0ef841bbbe 100644
--- a/compiler/rustc_codegen_ssa/src/back/link.rs
+++ b/compiler/rustc_codegen_ssa/src/back/link.rs
@@ -1931,7 +1931,12 @@ fn add_order_independent_options(
     // Try to strip as much out of the generated object by removing unused
     // sections if possible. See more comments in linker.rs
     if !sess.link_dead_code() {
-        let keep_metadata = crate_type == CrateType::Dylib;
+        // If PGO is enabled sometimes gc_sections will remove the profile data section
+        // as it appears to be unused. This can then cause the PGO profile file to lose
+        // some functions. If we are generating a profile we shouldn't strip those metadata
+        // sections to ensure we have all the data for PGO.
+        let keep_metadata =
+            crate_type == CrateType::Dylib || sess.opts.cg.profile_generate.enabled();
         cmd.gc_sections(keep_metadata);
     }