diff --git a/CHANGELOG.md b/CHANGELOG.md
index dd4c93ac051..b8cceaaaeed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,8 @@ Main (unreleased)
 - (_Public Preview_) Additions to `database_observability.mysql` component:
   - replace the internal `server_id` label attribution in favor of a hash composed from `@@server_uuid` and `@@hostname`
 
+- Fix the `prometheus.operator.*` components internal scrape manager now having a way to enable ingesting native histograms. (@dehaansa)
+
 v1.12.0
 -----------------
 
diff --git a/docs/sources/shared/reference/components/prom-operator-scrape.md b/docs/sources/shared/reference/components/prom-operator-scrape.md
index 612d442d73a..fb18aeb35b5 100644
--- a/docs/sources/shared/reference/components/prom-operator-scrape.md
+++ b/docs/sources/shared/reference/components/prom-operator-scrape.md
@@ -4,7 +4,8 @@ description: Shared content, prom operator scrape
 headless: true
 ---
 
-| Name                      | Type       | Description                                                                                                                  | Default | Required |
-| ------------------------- | ---------- | ---------------------------------------------------------------------------------------------------------------------------- | ------- | -------- |
-| `default_scrape_interval` | `duration` | The default interval between scraping targets. Used as the default if the target resource doesn't provide a scrape interval. | `1m`    | no       |
-| `default_scrape_timeout`  | `duration` | The default timeout for scrape requests. Used as the default if the target resource doesn't provide a scrape timeout.        | `10s`   | no       |
+| Name                       | Type       | Description                                                                                                                  | Default | Required |
+|----------------------------|------------|------------------------------------------------------------------------------------------------------------------------------|---------|----------|
+| `default_scrape_interval`  | `duration` | The default interval between scraping targets. Used as the default if the target resource doesn't provide a scrape interval. | `1m`    | no       |
+| `default_scrape_timeout`   | `duration` | The default timeout for scrape requests. Used as the default if the target resource doesn't provide a scrape timeout.        | `10s`   | no       |
+| `scrape_native_histograms` | `bool`     | Allow the scrape manager to ingest native histograms.                                                                        | `false` | no       |
diff --git a/internal/component/prometheus/operator/common/crdmanager.go b/internal/component/prometheus/operator/common/crdmanager.go
index b5948edf9ea..37f595186bd 100644
--- a/internal/component/prometheus/operator/common/crdmanager.go
+++ b/internal/component/prometheus/operator/common/crdmanager.go
@@ -146,7 +146,10 @@ func (c *crdManager) Run(ctx context.Context) error {
 
 	// Start prometheus scrape manager.
 	alloyAppendable := prometheus.NewFanout(c.args.ForwardTo, c.opts.ID, c.opts.Registerer, c.ls)
-	opts := &scrape.Options{}
+
+	opts := &scrape.Options{
+		EnableNativeHistogramsIngestion: c.args.Scrape.ScrapeNativeHistograms,
+	}
 	c.scrapeManager, err = scrape.NewManager(opts, slog.New(logging.NewSlogGoKitHandler(c.logger)), nil, alloyAppendable, unregisterer)
 	if err != nil {
 		return fmt.Errorf("creating scrape manager: %w", err)
diff --git a/internal/component/prometheus/operator/configgen/config_gen.go b/internal/component/prometheus/operator/configgen/config_gen.go
index 8b712a6d488..df93414be6c 100644
--- a/internal/component/prometheus/operator/configgen/config_gen.go
+++ b/internal/component/prometheus/operator/configgen/config_gen.go
@@ -190,6 +190,10 @@ func (cg *ConfigGenerator) generateDefaultScrapeConfig() *config.ScrapeConfig {
 		c.ScrapeTimeout = model.Duration(opt.DefaultScrapeTimeout)
 	}
 
+	if opt.ScrapeNativeHistograms {
+		c.ScrapeProtocols = config.DefaultProtoFirstScrapeProtocols
+	}
+
 	return &c
 }
 
diff --git a/internal/component/prometheus/operator/configgen/config_gen_podmonitor_test.go b/internal/component/prometheus/operator/configgen/config_gen_podmonitor_test.go
index 16634bdf167..d405de202ca 100644
--- a/internal/component/prometheus/operator/configgen/config_gen_podmonitor_test.go
+++ b/internal/component/prometheus/operator/configgen/config_gen_podmonitor_test.go
@@ -529,8 +529,9 @@ func TestGeneratePodMonitorConfig(t *testing.T) {
 					{TargetLabel: "__meta_foo", Replacement: "bar"},
 				},
 				ScrapeOptions: operator.ScrapeOptions{
-					DefaultScrapeInterval: time.Hour,
-					DefaultScrapeTimeout:  42 * time.Second,
+					DefaultScrapeInterval:  time.Hour,
+					DefaultScrapeTimeout:   42 * time.Second,
+					ScrapeNativeHistograms: false,
 				},
 			}
 			cfg, err := cg.GeneratePodMonitorConfig(tc.m, tc.ep, 1)
diff --git a/internal/component/prometheus/operator/configgen/config_gen_scrapeconfig_test.go b/internal/component/prometheus/operator/configgen/config_gen_scrapeconfig_test.go
index 3139ef6acd6..f59b1791612 100644
--- a/internal/component/prometheus/operator/configgen/config_gen_scrapeconfig_test.go
+++ b/internal/component/prometheus/operator/configgen/config_gen_scrapeconfig_test.go
@@ -217,8 +217,9 @@ func TestGenerateStaticScrapeConfigConfig(t *testing.T) {
 					{TargetLabel: "__meta_foo", Replacement: "bar"},
 				},
 				ScrapeOptions: operator.ScrapeOptions{
-					DefaultScrapeInterval: time.Hour,
-					DefaultScrapeTimeout:  42 * time.Second,
+					DefaultScrapeInterval:  time.Hour,
+					DefaultScrapeTimeout:   42 * time.Second,
+					ScrapeNativeHistograms: false,
 				},
 			}
 			cfg, err := cg.generateStaticScrapeConfigConfig(tc.m, tc.ep, 1)
diff --git a/internal/component/prometheus/operator/types.go b/internal/component/prometheus/operator/types.go
index 7f0005eb19a..c4b8d5baaf0 100644
--- a/internal/component/prometheus/operator/types.go
+++ b/internal/component/prometheus/operator/types.go
@@ -49,6 +49,9 @@ type ScrapeOptions struct {
 
 	// DefaultScrapeTimeout is the default timeout to scrape targets.
 	DefaultScrapeTimeout time.Duration `alloy:"default_scrape_timeout,attr,optional"`
+
+	// ScrapeNativeHistograms enables scraping of Prometheus native histograms.
+	ScrapeNativeHistograms bool `alloy:"scrape_native_histograms,attr,optional"`
 }
 
 func (s *ScrapeOptions) GlobalConfig() promconfig.GlobalConfig {