diff --git a/src/wasm/wasm-binary.cpp b/src/wasm/wasm-binary.cpp
index d24f7da423f..9cc55af0522 100644
--- a/src/wasm/wasm-binary.cpp
+++ b/src/wasm/wasm-binary.cpp
@@ -1373,9 +1373,19 @@ void WasmBinaryWriter::writeSourceMapEpilog() {
 
 void WasmBinaryWriter::writeLateCustomSections() {
   for (auto& section : wasm->customSections) {
-    if (section.name != BinaryConsts::CustomSections::Dylink) {
-      writeCustomSection(section);
+    if (section.name == BinaryConsts::CustomSections::Dylink) {
+      // This is an early custom section.
+      continue;
     }
+
+    if (section.name == BinaryConsts::CustomSections::SourceMapUrl &&
+        sourceMap && !sourceMapUrl.empty()) {
+      // We are writing a SourceMapURL manually, following the user's request.
+      // Do not emit the existing custom section as a second one.
+      continue;
+    }
+
+    writeCustomSection(section);
   }
 }
 
diff --git a/test/lit/debug/source-map-url.wast b/test/lit/debug/source-map-url.wast
new file mode 100644
index 00000000000..906ae8efb61
--- /dev/null
+++ b/test/lit/debug/source-map-url.wast
@@ -0,0 +1,37 @@
+(module
+  (func $test (param i32) (result i32)
+    ;;@ waka:100:1
+    (i32.const 42)
+  )
+)
+
+;; 1. Generate a binary with a source map and url.
+;;
+;; RUN: wasm-opt %s -g -o %t.wasm -osm %t.wasm.map -osu=one
+;; RUN: wasm-dis %t.wasm | filecheck %s --check-prefix=ONE
+
+;; ONE:  ;; custom section "sourceMappingURL", size 4
+
+
+;; 2. Round-trip that binary, again using -osu. This should not end up with two
+;; sourceMappingURL sections (one could arrive from the flag, and one from the
+;; existing custom section, if we copy it). Note the length increases, from
+;; "one\0" (4) to "swap\0" (5), as we swap the URL.
+;;
+;; RUN: wasm-opt %t.wasm -o %t.wasm2 -ism %t.wasm.map -osm %t.wasm.map2 -osu=swap
+;; RUN: wasm-dis %t.wasm2 | filecheck %s --check-prefix=SWAP
+
+;; Look for a wrong section both before and after the correct one.
+
+;; SWAP-NOT:  ;; custom section "sourceMappingURL", size 4
+;; SWAP:  ;; custom section "sourceMappingURL", size 5
+;; SWAP-NOT:  ;; custom section "sourceMappingURL"
+
+
+;; 3. Round-trip without -osu. Now we just copy the old URL.
+;;
+;; RUN: wasm-opt %t.wasm2 -o %t.wasm3 -ism %t.wasm.map2 -osm %t.wasm.map3
+;; RUN: wasm-dis %t.wasm3 | filecheck %s --check-prefix=ROUND
+
+;; ROUND:  ;; custom section "sourceMappingURL", size 5
+