diff --git a/CHANGELOG.md b/CHANGELOG.md
index ce247bf84b..1bd9aeb1ac 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -72,6 +72,7 @@ Ref: https://keepachangelog.com/en/1.0.0/
 
 ### Improvements
 
+* (server) [#16395](https://github.com/cosmos/cosmos-sdk/pull/16395) Do not override some Comet config is purposely set differently in `InterceptConfigsPreRunHandler`.
 * (types) [#16076](https://github.com/cosmos/cosmos-sdk/pull/16076) Optimize `ChainAnteDecorators`/`ChainPostDecorators` to instantiate the functions once instead of on every invocation of the returned `AnteHandler`/`PostHandler`.
 * (client) [#16075](https://github.com/cosmos/cosmos-sdk/pull/16075) Partly revert [#15953](https://github.com/cosmos/cosmos-sdk/issues/15953) and `factory.Prepare` does nothing in offline mode.
 * (server) [#16071](https://github.com/cosmos/cosmos-sdk/pull/16071) When `mempool.max-txs` is set to a negative value, use a no-op mempool (effectively disable the app mempool).
diff --git a/server/util.go b/server/util.go
index 14a94581e3..96119392f9 100644
--- a/server/util.go
+++ b/server/util.go
@@ -247,10 +247,16 @@ func interceptConfigs(rootViper *viper.Viper, customAppTemplate string, customCo
 			return nil, fmt.Errorf("error in config file: %w", err)
 		}
 
-		conf.RPC.PprofListenAddress = "localhost:6060"
-		conf.P2P.RecvRate = 5120000
-		conf.P2P.SendRate = 5120000
-		conf.Consensus.TimeoutCommit = 5 * time.Second
+		defaultCometCfg := cmtcfg.DefaultConfig()
+		// The SDK is opinionated about those comet values, so we set them here.
+		// We verify first that the user has not changed them for not overriding them.
+		if conf.Consensus.TimeoutCommit == defaultCometCfg.Consensus.TimeoutCommit {
+			conf.Consensus.TimeoutCommit = 5 * time.Second
+		}
+		if conf.RPC.PprofListenAddress == defaultCometCfg.RPC.PprofListenAddress {
+			conf.RPC.PprofListenAddress = "localhost:6060"
+		}
+
 		cmtcfg.WriteConfigFile(cmtCfgFile, conf)
 
 	case err != nil: