diff --git a/tools/src/cmd/cts/format/format.go b/tools/src/cmd/cts/format/format.go
index 823e1bea1c..bb2aa702de 100644
--- a/tools/src/cmd/cts/format/format.go
+++ b/tools/src/cmd/cts/format/format.go
@@ -51,5 +51,11 @@ func (c *cmd) Run(ctx context.Context, cfg common.Config) error {
 	if err != nil {
 		return err
 	}
+
+	// Sort the expectations in each chunk.
+	for _, chunk := range ex.Chunks {
+		chunk.Expectations.Sort()
+	}
+
 	return ex.Save(c.flags.expectations)
 }
diff --git a/tools/src/cts/expectations/parse.go b/tools/src/cts/expectations/parse.go
index 42d16d026a..aafb800a4f 100644
--- a/tools/src/cts/expectations/parse.go
+++ b/tools/src/cts/expectations/parse.go
@@ -55,7 +55,6 @@ func Parse(body string) (Content, error) {
 	// flush completes the current chunk, appending it to 'content'
 	flush := func() {
 		parseTags(&content.Tags, pending.Comments)
-		pending.Expectations.Sort()
 		content.Chunks = append(content.Chunks, pending)
 		pending = Chunk{}
 	}
diff --git a/tools/src/cts/expectations/update_test.go b/tools/src/cts/expectations/update_test.go
index d85a9bc338..081ea11f97 100644
--- a/tools/src/cts/expectations/update_test.go
+++ b/tools/src/cts/expectations/update_test.go
@@ -169,8 +169,8 @@ a:b,c:* [ Failure ]
 		{ //////////////////////////////////////////////////////////////////////
 			name: "simple expectation with tags",
 			expectations: `
-[ gpu-b ] a:b,c:* [ Failure ]
 [ os-a ] a:b,c:* [ Failure ]
+[ gpu-b ] a:b,c:* [ Failure ]
 `,
 			results: result.List{
 				result.Result{
@@ -186,7 +186,7 @@ a:b,c:* [ Failure ]
 				{
 					Severity: expectations.Error,
 					Line:     headerLines + 3,
-					Message:  "[os-a] a:b,c:* collides with expectation at line 8",
+					Message:  "[gpu-b] a:b,c:* collides with expectation at line 8",
 				},
 			},
 		},
@@ -219,8 +219,8 @@ a:b,c:* [ Failure ]
 		{ //////////////////////////////////////////////////////////////////////
 			name: "collision with child-expectation",
 			expectations: `
-crbug.com/a/1 a:b:x:* [ Failure ]
-crbug.com/a/2 a:b:* [ Failure ]
+a:b:x:* [ Failure ]
+a:b:* [ Failure ]
 `,
 			results: result.List{
 				result.Result{
@@ -235,7 +235,7 @@ crbug.com/a/2 a:b:* [ Failure ]
 				},
 			},
 			updated: `
-crbug.com/a/1 a:b:x:* [ Failure ]
+a:b:x:* [ Failure ]
 
 # New failures. Please triage:
 crbug.com/dawn/0000 a:b:y:* [ Failure ]