diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index cdfb42b18..dfc06fd4e 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -202,9 +202,10 @@ func (c *flagConfig) setFeatureListOptions(logger log.Logger) error {
 				level.Info(logger).Log("msg", "No default port will be appended to scrape targets' addresses.")
 			case "native-histograms":
 				c.tsdb.EnableNativeHistograms = true
-				// Change global variable. Hacky, but it's hard to pass new option or default to unmarshaller.
+				// Change relevant global variables. Hacky, but it's hard to pass a new option or default to unmarshallers.
 				config.DefaultConfig.GlobalConfig.ScrapeProtocols = config.DefaultNativeHistogramScrapeProtocols
-				level.Info(logger).Log("msg", "Experimental native histogram support enabled. Changed default scrape_protocols to prefer PrometheusProto format.", "global.scrape_protocols", fmt.Sprintf("%v", config.DefaultConfig.GlobalConfig.ScrapeProtocols))
+				config.DefaultGlobalConfig.ScrapeProtocols = config.DefaultNativeHistogramScrapeProtocols
+				level.Info(logger).Log("msg", "Experimental native histogram support enabled. Changed default scrape_protocols to prefer PrometheusProto format.", "global.scrape_protocols", fmt.Sprintf("%v", config.DefaultGlobalConfig.ScrapeProtocols))
 			case "":
 				continue
 			case "promql-at-modifier", "promql-negative-offset":