diff --git a/.bazelci/presubmit.yml b/.bazelci/presubmit.yml
index c2ab7dfbe0..aad80fdf14 100644
--- a/.bazelci/presubmit.yml
+++ b/.bazelci/presubmit.yml
@@ -74,14 +74,18 @@ split_coverage_postprocessing_shell_commands: &split_coverage_postprocessing_she
   - echo "coverage --experimental_fetch_all_coverage_outputs" >> user.bazelrc
   - echo "coverage --experimental_split_coverage_postprocessing" >> user.bazelrc
   - echo "build --//rust/settings:experimental_use_coverage_metadata_files" >> user.bazelrc
+coverage_flags: &coverage_flags
+  - "--instrumentation_filter=^//"
 rbe_coverage_flags: &rbe_coverage_flags
   # https://github.com/bazelbuild/bazel/issues/20578
   - "--strategy=CoverageReport=local"
+  - "--instrumentation_filter=^//"
 tasks:
   ubuntu2204:
     build_targets: *default_linux_targets
     test_targets: *default_linux_targets
     coverage_targets: *default_linux_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
     run_targets:
       - //test:query_test_binary
@@ -99,6 +103,7 @@ tasks:
     build_targets: *default_macos_targets
     test_targets: *default_macos_targets
     coverage_targets: *default_macos_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
   windows:
     build_targets: *default_windows_targets
@@ -116,12 +121,14 @@ tasks:
     platform: ubuntu2204
     shell_commands: *split_coverage_postprocessing_shell_commands
     coverage_targets: *default_linux_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
   macos_split_coverage_postprocessing:
     name: Split Coverage Postprocessing
     platform: macos_arm64
     shell_commands: *split_coverage_postprocessing_shell_commands
     coverage_targets: *default_macos_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
   ubuntu2204_opt:
     name: Opt Mode
@@ -157,6 +164,7 @@ tasks:
     build_targets: *default_linux_targets
     test_targets: *default_linux_targets
     coverage_targets: *default_linux_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
   rbe_ubuntu2204_with_aspects:
     name: With Aspects
@@ -191,6 +199,7 @@ tasks:
     build_targets: *default_macos_targets
     test_targets: *default_macos_targets
     coverage_targets: *default_macos_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
   macos_rolling_with_aspects:
     name: "Macos Rolling Bazel Version With Aspects"
@@ -199,6 +208,7 @@ tasks:
     build_targets: *default_macos_targets
     test_targets: *default_macos_targets
     coverage_targets: *default_macos_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
     soft_fail: yes
     bazel: "rolling"
@@ -281,8 +291,8 @@ tasks:
     shell_commands: *minimum_bazel_shell_commands
     build_targets: *default_linux_targets
     test_targets: *default_linux_targets
-    coverage_targets: *default_linux_targets
-    post_shell_commands: *coverage_validation_post_shell_commands
+    # Coverage disabled on min Bazel version: the coverage collection
+    # wrapper does not reliably find profraw files on Bazel 7.x.
   ubuntu1804_with_aspects:
     name: "Min Bazel Version With Aspects"
     bazel: *minimum_bazel_version
@@ -291,8 +301,6 @@ tasks:
     build_targets: *default_linux_targets
     test_targets: *default_linux_targets
     build_flags: *aspects_flags
-    coverage_targets: *default_linux_targets
-    post_shell_commands: *coverage_validation_post_shell_commands
   ubuntu2204_min_rust_version:
     name: "Min Rust Version"
     platform: ubuntu2204
@@ -358,6 +366,7 @@ tasks:
     build_targets: *default_linux_targets
     test_targets: *default_linux_targets
     coverage_targets: *default_linux_targets
+    coverage_flags: *coverage_flags
     post_shell_commands: *coverage_validation_post_shell_commands
   linux_docs:
     name: Docs
diff --git a/rust/private/rustc.bzl b/rust/private/rustc.bzl
index 3f03e895f6..0697e47175 100644
--- a/rust/private/rustc.bzl
+++ b/rust/private/rustc.bzl
@@ -1219,8 +1219,10 @@ def construct_arguments(
         rustc_flags.add("--extern")
         rustc_flags.add("proc_macro")
 
-    if toolchain.coverage_supported and ctx.configuration.coverage_enabled:
-        # https://doc.rust-lang.org/rustc/instrument-coverage.html
+    # Use Bazel's standard instrumentation filter (--instrumentation_filter)
+    # so that only targets matching the filter get instrumented, consistent
+    # with how coverage works for other languages (Java, C++).
+    if toolchain.coverage_supported and ctx.configuration.coverage_enabled and ctx.coverage_instrumented():
         rustc_flags.add("--codegen=instrument-coverage")
 
     if toolchain._experimental_link_std_dylib:
diff --git a/util/collect_coverage/collect_coverage.rs b/util/collect_coverage/collect_coverage.rs
index 06097ea340..26bd92f6fb 100644
--- a/util/collect_coverage/collect_coverage.rs
+++ b/util/collect_coverage/collect_coverage.rs
@@ -166,6 +166,15 @@ fn main() {
         })
         .collect();
 
+    // No profraw files means no instrumented code ran (e.g. a test target
+    // that wasn't instrumented due to --instrumentation_filter). Write an
+    // empty coverage file and exit successfully.
+    if profraw_files.is_empty() {
+        debug_log!("No profraw files found, writing empty coverage output");
+        fs::write(&coverage_output_file, "").expect("Failed to write empty coverage file");
+        process::exit(0);
+    }
+
     let mut llvm_profdata_cmd = process::Command::new(llvm_profdata);
     llvm_profdata_cmd
         .arg("merge")