diff --git a/src/link/Wasm.zig b/src/link/Wasm.zig
index 81e73e6ecf..b7ed2c035f 100644
--- a/src/link/Wasm.zig
+++ b/src/link/Wasm.zig
@@ -110,7 +110,7 @@ func_types: std.ArrayListUnmanaged(std.wasm.Type) = .{},
 /// Output function section where the key is the original
 /// function index and the value is function.
 /// This allows us to map multiple symbols to the same function.
-functions: std.AutoArrayHashMapUnmanaged(struct { file: ?u16, index: u32 }, std.wasm.Func) = .{},
+functions: std.AutoArrayHashMapUnmanaged(struct { file: ?u16, index: u32 }, struct { func: std.wasm.Func, sym_index: u32 }) = .{},
 /// Output global section
 wasm_globals: std.ArrayListUnmanaged(std.wasm.Global) = .{},
 /// Memory section
@@ -1584,7 +1584,7 @@ fn getFunctionSignature(wasm: *const Wasm, loc: SymbolLoc) std.wasm.Type {
         const ty_index = wasm.imports.get(loc).?.kind.function;
         return wasm.func_types.items[ty_index];
     }
-    return wasm.func_types.items[wasm.functions.get(.{ .file = loc.file, .index = loc.index }).?.type_index];
+    return wasm.func_types.items[wasm.functions.get(.{ .file = loc.file, .index = symbol.index }).?.func.type_index];
 }
 
 /// Lowers a constant typed value to a local symbol and atom.
@@ -2141,7 +2141,7 @@ fn parseAtom(wasm: *Wasm, atom_index: Atom.Index, kind: Kind) !void {
             try wasm.functions.putNoClobber(
                 wasm.base.allocator,
                 .{ .file = null, .index = index },
-                .{ .type_index = type_index },
+                .{ .func = .{ .type_index = type_index }, .sym_index = atom.sym_index },
             );
             symbol.tag = .function;
             symbol.index = index;
@@ -2274,7 +2274,14 @@ fn allocateAtoms(wasm: *Wasm) !void {
         while (true) {
             const atom = wasm.getAtomPtr(atom_index);
             const symbol_loc = atom.symbolLoc();
-            const sym = symbol_loc.getSymbol(wasm);
+            // Ensure we get the original symbol, so we verify the correct symbol on whether
+            // it is dead or not and ensure an atom is removed when dead.
+            // This is required as we may have parsed aliases into atoms.
+            const sym = if (symbol_loc.file) |object_index| sym: {
+                const object = wasm.objects.items[object_index];
+                break :sym object.symtable[symbol_loc.index];
+            } else wasm.symbols.items[symbol_loc.index];
+
             if (sym.isDead()) {
                 // Dead symbols must be unlinked from the linked-list to prevent them
                 // from being emit into the binary.
@@ -2477,7 +2484,7 @@ fn initializeCallCtorsFunction(wasm: *Wasm) !void {
         // call constructors
         for (wasm.init_funcs.items) |init_func_loc| {
             const symbol = init_func_loc.getSymbol(wasm);
-            const func = wasm.functions.values()[symbol.index - wasm.imported_functions_count];
+            const func = wasm.functions.values()[symbol.index - wasm.imported_functions_count].func;
             const ty = wasm.func_types.items[func.type_index];
 
             // Call function by its function index
@@ -2519,7 +2526,7 @@ fn createSyntheticFunction(
     try wasm.functions.putNoClobber(
         wasm.base.allocator,
         .{ .file = null, .index = func_index },
-        .{ .type_index = ty_index },
+        .{ .func = .{ .type_index = ty_index }, .sym_index = loc.index },
     );
     symbol.index = func_index;
 
@@ -2740,6 +2747,9 @@ fn setupImports(wasm: *Wasm) !void {
 /// Takes the global, function and table section from each linked object file
 /// and merges it into a single section for each.
 fn mergeSections(wasm: *Wasm) !void {
+    var removed_duplicates = std.ArrayList(SymbolLoc).init(wasm.base.allocator);
+    defer removed_duplicates.deinit();
+
     for (wasm.resolved_symbols.keys()) |sym_loc| {
         if (sym_loc.file == null) {
             // Zig code-generated symbols are already within the sections and do not
@@ -2767,9 +2777,19 @@ fn mergeSections(wasm: *Wasm) !void {
                     wasm.base.allocator,
                     .{ .file = sym_loc.file, .index = symbol.index },
                 );
-                if (!gop.found_existing) {
-                    gop.value_ptr.* = object.functions[index];
+                if (gop.found_existing) {
+                    // We found an alias to the same function, discard this symbol in favor of
+                    // the original symbol and point the discard function to it. This ensures
+                    // we only emit a single function, instead of duplicates.
+                    try wasm.discarded.putNoClobber(
+                        wasm.base.allocator,
+                        sym_loc,
+                        .{ .file = gop.key_ptr.*.file, .index = gop.value_ptr.*.sym_index },
+                    );
+                    try removed_duplicates.append(sym_loc);
+                    continue;
                 }
+                gop.value_ptr.* = .{ .func = object.functions[index], .sym_index = sym_loc.index };
                 symbol.index = @as(u32, @intCast(gop.index)) + wasm.imported_functions_count;
             },
             .global => {
@@ -2786,6 +2806,12 @@ fn mergeSections(wasm: *Wasm) !void {
         }
     }
 
+    // For any removed duplicates, remove them from the resolved symbols list
+    for (removed_duplicates.items) |sym_loc| {
+        assert(wasm.resolved_symbols.swapRemove(sym_loc));
+        sym_loc.getSymbol(wasm).unmark();
+    }
+
     log.debug("Merged ({d}) functions", .{wasm.functions.count()});
     log.debug("Merged ({d}) globals", .{wasm.wasm_globals.items.len});
     log.debug("Merged ({d}) tables", .{wasm.tables.items.len});
@@ -2821,7 +2847,7 @@ fn mergeTypes(wasm: *Wasm) !void {
             import.kind.function = try wasm.putOrGetFuncType(original_type);
         } else if (!dirty.contains(symbol.index)) {
             log.debug("Adding type from function '{s}'", .{sym_loc.getName(wasm)});
-            const func = &wasm.functions.values()[symbol.index - wasm.imported_functions_count];
+            const func = &wasm.functions.values()[symbol.index - wasm.imported_functions_count].func;
             func.type_index = try wasm.putOrGetFuncType(object.func_types[func.type_index]);
             dirty.putAssumeCapacityNoClobber(symbol.index, {});
         }
@@ -3498,12 +3524,12 @@ fn linkWithZld(wasm: *Wasm, comp: *Compilation, prog_node: *std.Progress.Node) l
 
     try wasm.markReferences();
     try wasm.setupImports();
+    try wasm.mergeSections();
+    try wasm.mergeTypes();
     try wasm.allocateAtoms();
     try wasm.setupMemory();
     wasm.allocateVirtualAddresses();
     wasm.mapFunctionTable();
-    try wasm.mergeSections();
-    try wasm.mergeTypes();
     try wasm.initializeCallCtorsFunction();
     try wasm.setupInitMemoryFunction();
     try wasm.setupTLSRelocationsFunction();
@@ -3639,12 +3665,12 @@ pub fn flushModule(wasm: *Wasm, comp: *Compilation, prog_node: *std.Progress.Nod
         }
     }
 
+    try wasm.mergeSections();
+    try wasm.mergeTypes();
     try wasm.allocateAtoms();
     try wasm.setupMemory();
     wasm.allocateVirtualAddresses();
     wasm.mapFunctionTable();
-    try wasm.mergeSections();
-    try wasm.mergeTypes();
     try wasm.initializeCallCtorsFunction();
     try wasm.setupInitMemoryFunction();
     try wasm.setupTLSRelocationsFunction();
@@ -3745,7 +3771,7 @@ fn writeToFile(
     if (wasm.functions.count() != 0) {
         const header_offset = try reserveVecSectionHeader(&binary_bytes);
         for (wasm.functions.values()) |function| {
-            try leb.writeULEB128(binary_writer, function.type_index);
+            try leb.writeULEB128(binary_writer, function.func.type_index);
         }
 
         try writeVecSectionHeader(
@@ -3916,6 +3942,7 @@ fn writeToFile(
             sorted_atoms.appendAssumeCapacity(atom); // found more code atoms than functions
             atom_index = atom.prev orelse break;
         }
+        std.debug.assert(wasm.functions.count() == sorted_atoms.items.len);
 
         const atom_sort_fn = struct {
             fn sort(ctx: *const Wasm, lhs: *const Atom, rhs: *const Atom) bool {
diff --git a/src/link/Wasm/Symbol.zig b/src/link/Wasm/Symbol.zig
index b4507f9e14..75c26ca10d 100644
--- a/src/link/Wasm/Symbol.zig
+++ b/src/link/Wasm/Symbol.zig
@@ -100,6 +100,10 @@ pub fn mark(symbol: *Symbol) void {
     symbol.flags |= @intFromEnum(Flag.alive);
 }
 
+pub fn unmark(symbol: *Symbol) void {
+    symbol.flags &= ~@intFromEnum(Flag.alive);
+}
+
 pub fn isAlive(symbol: Symbol) bool {
     return symbol.flags & @intFromEnum(Flag.alive) != 0;
 }