diff --git a/src/lib/libbase64.js b/src/lib/libbase64.js
index 48546622878f1..3f0739e9d155c 100644
--- a/src/lib/libbase64.js
+++ b/src/lib/libbase64.js
@@ -8,18 +8,20 @@ addToLibrary({
   // Decodes a _known valid_ base64 string (without validation) and returns it as a new Uint8Array.
   // Benchmarked to be around 5x faster compared to a simple
   // "Uint8Array.from(atob(b64), c => c.charCodeAt(0))" (TODO: perhaps use this form in -Oz builds?)
+#if !JS_BASE64_API
   $base64Decode__postset: `
   // Precreate a reverse lookup table from chars
   // "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/" back to
   // bytes to make decoding fast.
-  for (var base64ReverseLookup = new Uint8Array(123/*'z'+1*/), i = 25; i >= 0; --i) {
-    base64ReverseLookup[48+i] = 52+i; // '0-9'
-    base64ReverseLookup[65+i] = i; // 'A-Z'
-    base64ReverseLookup[97+i] = 26+i; // 'a-z'
+  for (var base64ReverseLookup = new Uint8Array(123/*'z'+1*/), __b64i = 25; __b64i >= 0; --__b64i) {
+    base64ReverseLookup[48+__b64i] = 52+__b64i; // '0-9'
+    base64ReverseLookup[65+__b64i] = __b64i; // 'A-Z'
+    base64ReverseLookup[97+__b64i] = 26+__b64i; // 'a-z'
   }
   base64ReverseLookup[43] = 62; // '+'
   base64ReverseLookup[47] = 63; // '/'
 `,
+#endif
   $base64Decode__docs: '/** @noinline */',
   $base64Decode: (b64) => {
 #if JS_BASE64_API
diff --git a/test/codesize/test_codesize_hello_single_file.json b/test/codesize/test_codesize_hello_single_file.json
index 531826ef78b44..44dea2cde8813 100644
--- a/test/codesize/test_codesize_hello_single_file.json
+++ b/test/codesize/test_codesize_hello_single_file.json
@@ -1,6 +1,6 @@
 {
-  "a.out.js": 5371,
-  "a.out.js.gz": 2984,
+  "a.out.js": 5273,
+  "a.out.js.gz": 2921,
   "sent": [
     "a (fd_write)"
   ]
diff --git a/test/codesize/test_minimal_runtime_code_size_hello_webgl2_wasm_singlefile.json b/test/codesize/test_minimal_runtime_code_size_hello_webgl2_wasm_singlefile.json
index 819c402815ee8..3d2402f8aff1b 100644
--- a/test/codesize/test_minimal_runtime_code_size_hello_webgl2_wasm_singlefile.json
+++ b/test/codesize/test_minimal_runtime_code_size_hello_webgl2_wasm_singlefile.json
@@ -1,4 +1,4 @@
 {
-  "a.html": 15140,
-  "a.html.gz": 9079
+  "a.html": 15046,
+  "a.html.gz": 9018
 }
diff --git a/test/codesize/test_minimal_runtime_code_size_random_printf_wasm.json b/test/codesize/test_minimal_runtime_code_size_random_printf_wasm.json
index 61f7f42ba4aff..41ce4cfdd5704 100644
--- a/test/codesize/test_minimal_runtime_code_size_random_printf_wasm.json
+++ b/test/codesize/test_minimal_runtime_code_size_random_printf_wasm.json
@@ -1,4 +1,4 @@
 {
-  "a.html": 10982,
-  "a.html.gz": 5743
+  "a.html": 10884,
+  "a.html.gz": 5674
 }
diff --git a/tools/link.py b/tools/link.py
index 4303f257ea9dc..54f44551cfed7 100644
--- a/tools/link.py
+++ b/tools/link.py
@@ -1957,7 +1957,7 @@ def phase_emscript(in_wasm, wasm_target, js_syms, base_metadata):
 
   # No need to support base64 embedding in wasm2js mode since
   # the module is already in JS format.
-  if settings.SINGLE_FILE and not settings.WASM2JS:
+  if settings.SINGLE_FILE and not settings.SINGLE_FILE_BINARY_ENCODE and not settings.WASM2JS:
     settings.SUPPORT_BASE64_EMBEDDING = 1
     settings.DEFAULT_LIBRARY_FUNCS_TO_INCLUDE.append('$base64Decode')