diff --git a/docs/changelog.md b/docs/changelog.md
index 9332687a..490af22a 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,5 +1,12 @@
 # Changelog
 
+## v0.42.2
+
+### Fixed
+
+- `alerts/template` check didn't correctly handle `label_replace()` calls
+  in queries - #568.
+
 ## v0.42.1
 
 ### Fixed
diff --git a/internal/checks/alerts_template.go b/internal/checks/alerts_template.go
index 1fb07665..94a0ca1d 100644
--- a/internal/checks/alerts_template.go
+++ b/internal/checks/alerts_template.go
@@ -108,6 +108,16 @@ func (c TemplateCheck) Check(ctx context.Context, path string, rule parser.Rule,
 			safeLabels = append(safeLabels, be.VectorMatching.Include...)
 		}
 	}
+	for _, cl := range calls(rule.AlertingRule.Expr.Query, "label_replace") {
+		for i, v := range cl.Args {
+			if i == 1 {
+				if s, ok := v.(*promParser.StringLiteral); ok {
+					safeLabels = append(safeLabels, s.Val)
+				}
+				break
+			}
+		}
+	}
 
 	data := promTemplate.AlertTemplateData(map[string]string{}, map[string]string{}, "", 0)
 
@@ -477,11 +487,8 @@ func checkMetricLabels(msg, name, text string, metricLabels []string, excludeLab
 						found = true
 					}
 				}
-				if found && slices.Contains(safeLabels, v[1]) {
-					found = !excludeLabels
-				}
 				if found == excludeLabels {
-					if _, ok := done[v[1]]; !ok {
+					if _, ok := done[v[1]]; !ok && !slices.Contains(safeLabels, v[1]) {
 						msgs = append(msgs, fmt.Sprintf(msg, v[1]))
 						done[v[1]] = struct{}{}
 					}
@@ -539,3 +546,15 @@ func binaryExprs(node *parser.PromQLNode) (be []*promParser.BinaryExpr) {
 
 	return be
 }
+
+func calls(node *parser.PromQLNode, name string) (cl []*promParser.Call) {
+	if n, ok := node.Node.(*promParser.Call); ok && n.Func.Name == name {
+		cl = append(cl, n)
+	}
+
+	for _, child := range node.Children {
+		cl = append(cl, calls(child, name)...)
+	}
+
+	return cl
+}
diff --git a/internal/checks/alerts_template_test.go b/internal/checks/alerts_template_test.go
index 01e55abd..a539caeb 100644
--- a/internal/checks/alerts_template_test.go
+++ b/internal/checks/alerts_template_test.go
@@ -426,6 +426,22 @@ func TestTemplateCheck(t *testing.T) {
 				}
 			},
 		},
+		{
+			description: "don't trigger for label_replace() provided labels",
+			content: `
+- alert: label_replace_not_checked_correctly
+  expr: |
+    label_replace(
+      sum by (pod) (pod_status) > 0
+      ,"cluster", "$1", "pod", "(.*)"
+    )
+  annotations:
+    summary: "Some error found in {{ $labels.cluster }}"
+`,
+			checker:    newTemplateCheck,
+			prometheus: noProm,
+			problems:   noProblems,
+		},
 		{
 			description: "annotation label present on metrics (absent)",
 			content: `