diff --git a/config/toml.go b/config/toml.go
index 6f0c699c6f..a43773630a 100644
--- a/config/toml.go
+++ b/config/toml.go
@@ -480,6 +480,8 @@ only_internal_wal = "{{ .Consensus.OnlyInternalWal }}"
 wal_file = "{{ js .Consensus.WalPath }}"
 
 # How long we wait for a proposal block before prevoting nil
+# Deprecated: timeout_commit is overridden by the state machine in app version >= 3.
+# Therefore, the value set in this config will be ignored.
 timeout_propose = "{{ .Consensus.TimeoutPropose }}"
 # How much timeout_propose increases with each round
 timeout_propose_delta = "{{ .Consensus.TimeoutProposeDelta }}"
@@ -494,6 +496,8 @@ timeout_precommit_delta = "{{ .Consensus.TimeoutPrecommitDelta }}"
 # How long we wait after committing a block, before starting on the new
 # height (this gives us a chance to receive some more precommits, even
 # though we already have +2/3).
+# Deprecated: timeout_commit is overridden by the state machine in app version >= 3.
+# Therefore, the value set in this config will be ignored.
 timeout_commit = "{{ .Consensus.TimeoutCommit }}"
 
 # How many blocks to look back to check existence of the node's consensus votes before joining consensus