diff --git a/pkg/functions/client.go b/pkg/functions/client.go
index d8a7a11de7..75a5e8d3d7 100644
--- a/pkg/functions/client.go
+++ b/pkg/functions/client.go
@@ -691,6 +691,13 @@ func BuildWithPlatforms(pp []Platform) BuildOption {
 // not contain a populated Image.
 func (c *Client) Build(ctx context.Context, f Function, options ...BuildOption) (Function, error) {
 	fmt.Fprintf(os.Stderr, "Building function image\n")
+
+	// Warn if a func-generated legacy .s2i/bin/assemble file is left at the
+	// function root.  This runs on every build (and therefore every deploy,
+	// which uses build under the hood) so users see the warning regardless
+	// of which builder they switched to.
+	WarnIfLegacyS2IScaffolding(f, os.Stderr)
+
 	ctx, cancel := context.WithCancel(ctx)
 	defer cancel()
 
diff --git a/pkg/functions/function.go b/pkg/functions/function.go
index 07504c1103..f1b7253b55 100644
--- a/pkg/functions/function.go
+++ b/pkg/functions/function.go
@@ -3,6 +3,7 @@ package functions
 import (
 	"errors"
 	"fmt"
+	"io"
 	"os"
 	"path/filepath"
 	"reflect"
@@ -601,6 +602,29 @@ func (f Function) HasScaffolding() bool {
 	return f.Runtime == "go" || f.Runtime == "python"
 }
 
+// WarnIfLegacyS2IScaffolding writes a warning to w when the func-generated
+// legacy .s2i/bin/assemble file is present at the function root.
+// Prior to https://github.com/knative/func/pull/3436, func wrote S2I
+// scaffolding for go/python to <func-root>/.s2i/bin/assemble; it now lives
+// at .func/build/bin/assemble.  The stale file can interfere with other
+// builders (e.g. pack erroneously detects the assemble script).
+// The check is intentionally scoped to scaffolded runtimes (go/python) and
+// to the exact file func generated, so user-managed .s2i directories are not
+// flagged.
+func WarnIfLegacyS2IScaffolding(f Function, w io.Writer) {
+	if !f.HasScaffolding() {
+		return
+	}
+	legacyAssemble := filepath.Join(f.Root, ".s2i", "bin", "assemble")
+	if _, err := os.Stat(legacyAssemble); err == nil {
+		fmt.Fprintf(w, "Warning: a '.s2i/bin/assemble' file was detected at the function root. "+
+			"This appears to be leftover func-generated scaffolding from before it was moved to '%s/%s/bin/assemble'. "+
+			"It may interfere with other builders. "+
+			"If it was generated by func, consider removing '.s2i/' after verifying it is no longer needed.\n",
+			RunDataDir, BuildDir)
+	}
+}
+
 // LabelsMap combines default labels with the labels slice provided.
 // It will the resulting slice with ValidateLabels and return a key/value map.
 //   - key: EXAMPLE1                            # Label directly from a value
diff --git a/pkg/functions/function_unit_test.go b/pkg/functions/function_unit_test.go
index 7a0715db9e..a5b19b7a03 100644
--- a/pkg/functions/function_unit_test.go
+++ b/pkg/functions/function_unit_test.go
@@ -1,9 +1,11 @@
 package functions_test
 
 import (
+	"bytes"
 	"os"
 	"path/filepath"
 	"reflect"
+	"strings"
 	"testing"
 
 	"gopkg.in/yaml.v2"
@@ -296,3 +298,63 @@ func expectedDefaultLabels(f fn.Function) map[string]string {
 		fnlabels.FunctionRuntimeKey: f.Runtime,
 	}
 }
+
+// TestWarnIfLegacyS2IScaffolding ensures the warning is emitted only when a
+// func-generated legacy .s2i/bin/assemble file is present at the function root
+// for a scaffolded runtime (go/python).
+func TestWarnIfLegacyS2IScaffolding(t *testing.T) {
+	tests := []struct {
+		name        string
+		runtime     string
+		createFile  bool
+		wantWarning bool
+	}{
+		{
+			name:        "scaffolded runtime with legacy assemble warns",
+			runtime:     "go",
+			createFile:  true,
+			wantWarning: true,
+		},
+		{
+			name:        "non-scaffolded runtime with .s2i/bin/assemble does not warn",
+			runtime:     "node",
+			createFile:  true,
+			wantWarning: false,
+		},
+		{
+			name:        "scaffolded runtime without legacy assemble does not warn",
+			runtime:     "go",
+			createFile:  false,
+			wantWarning: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			root, cleanup := Mktemp(t)
+			t.Cleanup(cleanup)
+
+			if tt.createFile {
+				binDir := filepath.Join(root, ".s2i", "bin")
+				if err := os.MkdirAll(binDir, 0755); err != nil {
+					t.Fatal(err)
+				}
+				if err := os.WriteFile(filepath.Join(binDir, "assemble"), []byte("#!/bin/bash"), 0700); err != nil {
+					t.Fatal(err)
+				}
+			}
+
+			f := fn.Function{Root: root, Runtime: tt.runtime}
+			var buf bytes.Buffer
+			fn.WarnIfLegacyS2IScaffolding(f, &buf)
+
+			warned := strings.Contains(buf.String(), ".s2i/bin/assemble")
+			if tt.wantWarning && !warned {
+				t.Fatalf("expected a warning about .s2i/bin/assemble, got: %q", buf.String())
+			}
+			if !tt.wantWarning && warned {
+				t.Fatalf("unexpected warning about .s2i/bin/assemble: %q", buf.String())
+			}
+		})
+	}
+}
diff --git a/pkg/pipelines/tekton/pipelines_provider.go b/pkg/pipelines/tekton/pipelines_provider.go
index 540f995c0d..c51fd198ed 100644
--- a/pkg/pipelines/tekton/pipelines_provider.go
+++ b/pkg/pipelines/tekton/pipelines_provider.go
@@ -113,6 +113,11 @@ func (pp *PipelinesProvider) Run(ctx context.Context, f fn.Function) (string, fn
 		return "", f, err
 	}
 
+	// Warn if the func-generated legacy .s2i/bin/assemble exists; it will be
+	// uploaded to the PVC and can interfere with the in-cluster build.
+	// Remote deploy doesn't go through Client.Build, so we re-check here.
+	fn.WarnIfLegacyS2IScaffolding(f, os.Stderr)
+
 	// Namespace is either a new namespace, specified as f.Namespace, or
 	// the currently deployed namespace, recorded on f.Deploy.Namespace.
 	// If neither exist, an error is returned (namespace is required)