diff --git a/cmd/qa/cmd_health.go b/cmd/qa/cmd_health.go
index a90d91d..2ba99c4 100644
--- a/cmd/qa/cmd_health.go
+++ b/cmd/qa/cmd_health.go
@@ -105,20 +105,21 @@ func runHealth() error {
 	}
 
 	repoList := reg.List()
-	healthResults := make([]RepoHealth, 0, len(repoList))
+	allHealthResults := make([]RepoHealth, 0, len(repoList))
 	for _, repo := range repoList {
 		health := fetchRepoHealth(reg.Org, repo.Name)
-		healthResults = append(healthResults, health)
+		allHealthResults = append(allHealthResults, health)
 	}
 
 	// Sort by severity first, then repo name for deterministic output.
-	slices.SortFunc(healthResults, func(a, b RepoHealth) int {
+	slices.SortFunc(allHealthResults, func(a, b RepoHealth) int {
 		if p := cmp.Compare(healthPriority(a.Status), healthPriority(b.Status)); p != 0 {
 			return p
 		}
 		return strings.Compare(a.Name, b.Name)
 	})
 
+	healthResults := allHealthResults
 	if healthProblems {
 		problems := make([]RepoHealth, 0, len(healthResults))
 		for _, h := range healthResults {
@@ -129,7 +130,7 @@ func runHealth() error {
 		healthResults = problems
 	}
 
-	summary := summariseHealthResults(len(repoList), healthResults, healthProblems)
+	summary := summariseHealthResults(len(repoList), len(healthResults), allHealthResults, healthProblems)
 	if healthJSON {
 		return printHealthJSON(summary, healthResults)
 	}
@@ -264,10 +265,10 @@ func healthPriority(status string) int {
 	}
 }
 
-func summariseHealthResults(totalRepos int, results []RepoHealth, problemsOnly bool) HealthSummary {
+func summariseHealthResults(totalRepos int, filteredRepos int, results []RepoHealth, problemsOnly bool) HealthSummary {
 	summary := HealthSummary{
 		TotalRepos:    totalRepos,
-		FilteredRepos: len(results),
+		FilteredRepos: filteredRepos,
 		ByStatus:      make(map[string]int),
 		ProblemsOnly:  problemsOnly,
 	}
diff --git a/cmd/qa/cmd_health_test.go b/cmd/qa/cmd_health_test.go
index f33252c..4ee3429 100644
--- a/cmd/qa/cmd_health_test.go
+++ b/cmd/qa/cmd_health_test.go
@@ -83,6 +83,76 @@ esac
 	assert.NotContains(t, output, `"FailingSince"`)
 }
 
+func TestRunHealthJSONOutput_ProblemsOnlyKeepsOverallSummary(t *testing.T) {
+	dir := t.TempDir()
+	writeTestFile(t, filepath.Join(dir, "repos.yaml"), `version: 1
+org: forge
+base_path: .
+repos:
+  alpha:
+    type: module
+  beta:
+    type: module
+`)
+	writeExecutable(t, filepath.Join(dir, "gh"), `#!/bin/sh
+case "$*" in
+  *"--repo forge/alpha"*)
+    cat <<'JSON'
+[
+  {
+    "status": "completed",
+    "conclusion": "success",
+    "name": "CI",
+    "headSha": "abc123",
+    "updatedAt": "2026-03-30T00:00:00Z",
+    "url": "https://example.com/alpha/run/1"
+  }
+]
+JSON
+    ;;
+  *"--repo forge/beta"*)
+    printf '%s\n' 'simulated workflow lookup failure' >&2
+    exit 1
+    ;;
+  *)
+    printf '%s\n' "unexpected gh invocation: $*" >&2
+    exit 1
+    ;;
+esac
+`)
+
+	restoreWorkingDir(t, dir)
+	prependPath(t, dir)
+	resetHealthFlags(t)
+	t.Cleanup(func() {
+		healthRegistry = ""
+	})
+
+	parent := &cli.Command{Use: "qa"}
+	addHealthCommand(parent)
+	command := findSubcommand(t, parent, "health")
+	require.NoError(t, command.Flags().Set("registry", filepath.Join(dir, "repos.yaml")))
+	require.NoError(t, command.Flags().Set("json", "true"))
+	require.NoError(t, command.Flags().Set("problems", "true"))
+
+	output := captureStdout(t, func() {
+		require.NoError(t, command.RunE(command, nil))
+	})
+
+	var payload HealthOutput
+	require.NoError(t, json.Unmarshal([]byte(output), &payload))
+	assert.Equal(t, 2, payload.Summary.TotalRepos)
+	assert.Equal(t, 1, payload.Summary.Passing)
+	assert.Equal(t, 1, payload.Summary.Errors)
+	assert.Equal(t, 1, payload.Summary.FilteredRepos)
+	assert.True(t, payload.Summary.ProblemsOnly)
+	assert.Equal(t, 1, payload.Summary.ByStatus["passing"])
+	assert.Equal(t, 1, payload.Summary.ByStatus["error"])
+	require.Len(t, payload.Repos, 1)
+	assert.Equal(t, "error", payload.Repos[0].Status)
+	assert.Equal(t, "beta", payload.Repos[0].Name)
+}
+
 func TestRunHealthHumanOutput_ShowsFetchErrorsAsErrors(t *testing.T) {
 	dir := t.TempDir()
 	writeTestFile(t, filepath.Join(dir, "repos.yaml"), `version: 1