diff --git a/CHANGELOG.md b/CHANGELOG.md
index 89d540eaf2..071ed2ef68 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
 # Changelog
 
 ## unreleased
+ * [ENHANCEMENT] Scraping: add warning if targets relabel to same labels. This is enabled under the feature-flag `warn-if-targets-relabelled-to-same-labels`. #9589
 
 ## 3.2.1 / 2025-02-25
 
diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index 4559d51837..40db744252 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -264,6 +264,9 @@ func (c *flagConfig) setFeatureListOptions(logger *slog.Logger) error {
 				config.DefaultConfig.GlobalConfig.ScrapeProtocols = config.DefaultProtoFirstScrapeProtocols
 				config.DefaultGlobalConfig.ScrapeProtocols = config.DefaultProtoFirstScrapeProtocols
 				logger.Info("Experimental created timestamp zero ingestion enabled. Changed default scrape_protocols to prefer PrometheusProto format.", "global.scrape_protocols", fmt.Sprintf("%v", config.DefaultGlobalConfig.ScrapeProtocols))
+			case "warn-if-targets-relabelled-to-same-labels":
+				c.scrape.EnableWarnIfTargetsRelabelledToSameLabels = true
+				logger.Info("Enabled warning if targets relabelled to same labels")
 			case "delayed-compaction":
 				c.tsdb.EnableDelayedCompaction = true
 				logger.Info("Experimental delayed compaction is enabled.")
diff --git a/scrape/manager.go b/scrape/manager.go
index 5ef5dccb99..51d4514b59 100644
--- a/scrape/manager.go
+++ b/scrape/manager.go
@@ -90,6 +90,9 @@ type Options struct {
 	// Optional HTTP client options to use when scraping.
 	HTTPClientOptions []config_util.HTTPClientOption
 
+	// Option to warn if targets relabelled to same labels
+	EnableWarnIfTargetsRelabelledToSameLabels bool
+
 	// private option for testability.
 	skipOffsetting bool
 }
@@ -205,6 +208,40 @@ func (m *Manager) reload() {
 	}
 	m.mtxScrape.Unlock()
 	wg.Wait()
+
+	if m.opts.EnableWarnIfTargetsRelabelledToSameLabels {
+		m.warnIfTargetsRelabelledToSameLabels()
+	}
+}
+
+func (m *Manager) warnIfTargetsRelabelledToSameLabels() {
+	m.mtxScrape.Lock()
+	defer m.mtxScrape.Unlock()
+
+	totalTargets := 0
+	for _, scrapePool := range m.scrapePools {
+		totalTargets += len(scrapePool.activeTargets)
+	}
+
+	activeTargets := make(map[string]*Target, totalTargets)
+	buf := [1024]byte{}
+	builder := labels.NewBuilder(labels.EmptyLabels())
+	for _, scrapePool := range m.scrapePools {
+		for _, target := range scrapePool.activeTargets {
+			lStr := string(target.labels.Bytes(buf[:]))
+			t, ok := activeTargets[lStr]
+			if !ok {
+				activeTargets[lStr] = target
+				continue
+			}
+			m.logger.Warn(
+				"Found targets with same labels after relabelling",
+				"target_one", t.DiscoveredLabels(builder).Get(model.AddressLabel),
+				"target_two", target.DiscoveredLabels(builder).Get(model.AddressLabel),
+				"labels", target.labels.String(),
+			)
+		}
+	}
 }
 
 // setOffsetSeed calculates a global offsetSeed per server relying on extra label set.
diff --git a/scrape/manager_test.go b/scrape/manager_test.go
index 96381fa736..309e9b7cad 100644
--- a/scrape/manager_test.go
+++ b/scrape/manager_test.go
@@ -622,6 +622,43 @@ func TestManagerTargetsUpdates(t *testing.T) {
 	}
 }
 
+func TestManagerDuplicateAfterRelabellingWarning(t *testing.T) {
+	var buf bytes.Buffer
+	writer := &buf
+	logger := promslog.New(&promslog.Config{Writer: writer})
+
+	opts := Options{EnableWarnIfTargetsRelabelledToSameLabels: true}
+	testRegistry := prometheus.NewRegistry()
+	m, err := NewManager(&opts, logger, nil, nil, testRegistry)
+	require.NoError(t, err)
+
+	m.scrapePools = map[string]*scrapePool{}
+	sp := &scrapePool{
+		activeTargets: map[uint64]*Target{},
+	}
+	targetScrapeCfg := &config.ScrapeConfig{
+		Scheme:         "https",
+		MetricsPath:    "/metrics",
+		JobName:        "job",
+		ScrapeInterval: model.Duration(time.Second),
+		ScrapeTimeout:  model.Duration(time.Second),
+	}
+	sp.activeTargets[uint64(0)] = &Target{
+		scrapeConfig: targetScrapeCfg,
+		tLabels:      map[model.LabelName]model.LabelValue{model.AddressLabel: "foo"},
+	}
+	sp.activeTargets[uint64(1)] = &Target{
+		scrapeConfig: targetScrapeCfg,
+		tLabels:      map[model.LabelName]model.LabelValue{model.AddressLabel: "bar"},
+	}
+	m.scrapePools["default"] = sp
+
+	m.reload()
+	require.Contains(t, buf.String(), "Found targets with same labels after relabelling")
+	require.Contains(t, buf.String(), "foo")
+	require.Contains(t, buf.String(), "bar")
+}
+
 func TestSetOffsetSeed(t *testing.T) {
 	getConfig := func(prometheus string) *config.Config {
 		cfgText := `