diff --git a/internal/requestflag/innerflag.go b/internal/requestflag/innerflag.go
index 528915f..866ce27 100644
--- a/internal/requestflag/innerflag.go
+++ b/internal/requestflag/innerflag.go
@@ -32,6 +32,8 @@ type InnerFlag[
 	// map[string]any before SetInnerField runs. The hint is ignored for typed outer
 	// flags whose zero value already carries a dispatchable reflect.Kind.
 	OuterIsArrayOfObjects bool
+
+	hasBeenSet bool
 }
 
 // GetDataAliases returns the aliases recognized when parsing inner field keys from piped or flag YAML.
@@ -89,6 +91,7 @@ func (f *InnerFlag[T]) Set(name string, rawVal string) error {
 
 		if settableInnerField, ok := f.OuterFlag.(SettableInnerField); ok {
 			settableInnerField.SetInnerField(f.InnerField, parsedValue)
+			f.hasBeenSet = true
 		} else {
 			return fmt.Errorf("Cannot set inner field on %v", f.OuterFlag)
 		}
@@ -106,7 +109,7 @@ func (f *InnerFlag[T]) String() string {
 }
 
 func (f *InnerFlag[T]) IsSet() bool {
-	return false
+	return f.hasBeenSet
 }
 
 func (f *InnerFlag[T]) Names() []string {
diff --git a/internal/requestflag/innerflag_precedence_test.go b/internal/requestflag/innerflag_precedence_test.go
new file mode 100644
index 0000000..ad63103
--- /dev/null
+++ b/internal/requestflag/innerflag_precedence_test.go
@@ -0,0 +1,36 @@
+package requestflag
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/urfave/cli/v3"
+)
+
+func TestInnerFlagCLIValueBeatsPipedData(t *testing.T) {
+	t.Parallel()
+
+	outer := &Flag[map[string]any]{
+		Name:     "address",
+		BodyPath: "address",
+	}
+	assert.NoError(t, outer.PreParse())
+
+	cityInner := &InnerFlag[string]{
+		Name:       "address.city",
+		InnerField: "city",
+		OuterFlag:  outer,
+	}
+	assert.NoError(t, cityInner.Set("address.city", "cli-value"))
+	assert.True(t, cityInner.IsSet())
+
+	data := map[string]any{
+		"address": map[string]any{"city": "piped-value"},
+	}
+	cmd := &cli.Command{Flags: []cli.Flag{outer, cityInner}}
+	assert.NoError(t, ApplyStdinDataToFlags(cmd, data))
+
+	outerVal, ok := outer.Get().(map[string]any)
+	assert.True(t, ok)
+	assert.Equal(t, "cli-value", outerVal["city"])
+}
diff --git a/internal/requestflag/requestflag.go b/internal/requestflag/requestflag.go
index 60736b4..37f485f 100644
--- a/internal/requestflag/requestflag.go
+++ b/internal/requestflag/requestflag.go
@@ -137,11 +137,9 @@ type RequestContents struct {
 
 func applyStdinDataToFlags(cmd *cli.Command, data map[string]any, onSet func(cli.Flag)) error {
 	for _, flag := range cmd.Flags {
-		if flag.IsSet() {
-			continue
-		}
-
-		// Handle inner flags: look for their value nested under the outer flag's body path.
+		// Handle inner flags before the generic IsSet check. InnerFlag tracks whether
+		// it has ever been set, while array-of-object precedence is scoped to the
+		// trailing element of the outer value.
 		if inner, ok := flag.(HasOuterFlag); ok {
 			outer, outerOk := inner.GetOuterFlag().(InRequest)
 			if !outerOk || outer.GetBodyPath() == "" {
@@ -179,6 +177,10 @@ func applyStdinDataToFlags(cmd *cli.Command, data map[string]any, onSet func(cli
 			continue
 		}
 
+		if flag.IsSet() {
+			continue
+		}
+
 		inReq, ok := flag.(InRequest)
 		if !ok {
 			continue
diff --git a/internal/requestflag/stdinprovenance_test.go b/internal/requestflag/stdinprovenance_test.go
index bffd0ab..27e966f 100644
--- a/internal/requestflag/stdinprovenance_test.go
+++ b/internal/requestflag/stdinprovenance_test.go
@@ -158,3 +158,36 @@ func TestApplyStdinDataToFlagsWithProvenancePreservesExplicitEmptyCollections(t
 		})
 	}
 }
+
+func TestApplyStdinDataToFlagsFillsUnsetFieldOnTrailingArrayElement(t *testing.T) {
+	t.Parallel()
+
+	outer := &Flag[[]map[string]any]{Name: "entries", BodyPath: "entries"}
+	typeFlag := &InnerFlag[string]{
+		Name:                  "entries.type",
+		InnerField:            "type",
+		OuterFlag:             outer,
+		OuterIsArrayOfObjects: true,
+	}
+	thresholdFlag := &InnerFlag[int64]{
+		Name:                  "entries.compact-threshold",
+		InnerField:            "compact_threshold",
+		OuterFlag:             outer,
+		OuterIsArrayOfObjects: true,
+	}
+	require.NoError(t, outer.PreParse())
+	require.NoError(t, typeFlag.Set(typeFlag.Name, "first"))
+	require.NoError(t, thresholdFlag.Set(thresholdFlag.Name, "10"))
+	require.NoError(t, typeFlag.Set(typeFlag.Name, "second"))
+
+	command := &cli.Command{Flags: []cli.Flag{outer, typeFlag, thresholdFlag}}
+	err := ApplyStdinDataToFlags(command, map[string]any{
+		"entries": map[string]any{"compact_threshold": 20},
+	})
+
+	require.NoError(t, err)
+	require.Equal(t, []map[string]any{
+		{"type": "first", "compact_threshold": int64(10)},
+		{"type": "second", "compact_threshold": int64(20)},
+	}, outer.Get())
+}