diff --git a/compiler/cgen.nim b/compiler/cgen.nim
index 58d5b44376..77a221c875 100644
--- a/compiler/cgen.nim
+++ b/compiler/cgen.nim
@@ -2170,6 +2170,8 @@ proc genInitCode(m: BModule) =
       else:
         prcBody.add(extract(m.thing.s(section)))
 
+  #echo "PRE INIT PROC ", m.module.name.s, " ", m.s[cfsVars].buf.len
+
   if m.preInitProc.s(cpsInit).buf.len > 0 or m.preInitProc.s(cpsStmts).buf.len > 0:
     # Give this small function its own scope
     prcBody.addScope():
@@ -2523,13 +2525,7 @@ proc shouldRecompile(m: BModule; code: Rope, cfile: Cfile): bool =
       rawMessage(m.config, errCannotOpenFile, cfile.cname.string)
     result = true
 
-# We need 2 different logics here: pending modules (including
-# 'nim__dat') may require file merging for the combination of dead code
-# elimination and incremental compilation! Non pending modules need no
-# such logic and in fact the logic hurts for the main module at least;
-# it would generate multiple 'main' procs, for instance.
-
-proc writeModule(m: BModule, pending: bool) =
+proc writeModule(m: BModule) =
   let cfile = getCFile(m)
   if moduleHasChanged(m.g.graph, m.module):
     genInitCode(m)
@@ -2674,6 +2670,6 @@ proc cgenWriteModules*(backend: RootRef, config: ConfigRef) =
   genForwardedProcs(g)
 
   for m in cgenModules(g):
-    m.writeModule(pending=true)
+    m.writeModule()
   writeMapping(config, g.mapping)
   if g.generatedHeader != nil: writeHeader(g.generatedHeader)
diff --git a/compiler/nifbackend.nim b/compiler/nifbackend.nim
index a22404d52e..96071669d8 100644
--- a/compiler/nifbackend.nim
+++ b/compiler/nifbackend.nim
@@ -92,10 +92,16 @@ proc generateCode*(g: ModuleGraph; mainFileIdx: FileIndex) =
   # Reset backend state
   resetForBackend(g)
 
+  # Ensure systemFileIdx is set up (might not be set in cmdNifC path)
+  if g.config.m.systemFileIdx == InvalidFileIdx:
+    g.config.m.systemFileIdx = msgs.fileInfoIdx(g.config,
+        g.config.libpath / RelativeFile"system.nim")
+
   # Load system module first - it's always needed and contains essential hooks
   var precompSys = PrecompiledModule(module: nil)
-  if g.config.m.systemFileIdx != InvalidFileIdx:
-    precompSys = moduleFromNifFile(g, g.config.m.systemFileIdx, loadFullAst=true)
+  let systemFileIdx = g.config.m.systemFileIdx
+  if systemFileIdx != InvalidFileIdx:
+    precompSys = moduleFromNifFile(g, systemFileIdx, loadFullAst=true)
     g.systemModule = precompSys.module
 
   # Load all modules in dependency order using stack traversal
@@ -117,19 +123,16 @@ proc generateCode*(g: ModuleGraph; mainFileIdx: FileIndex) =
       discard setupNifBackendModule(g, precompSys.module)
     generateCodeForModule(g, precompSys)
 
-  # Generate code for all modules except main (main goes last)
-  # This ensures all modules are added to modulesClosed
+  # Track which modules have been processed to avoid duplicates
+  var processed = initIntSet()
+  if precompSys.module != nil:
+    processed.incl precompSys.module.position
 
+  # Generate code for all modules (skip system since it's already processed)
   for m in modules:
-    if m.module != g.systemModule:
+    if not processed.containsOrIncl(m.module.position):
       generateCodeForModule(g, m)
 
-  for m in BModuleList(g.backend).modules:
-    if m != nil:
-      assert m.module != nil
-      if sfMainModule notin m.module.flags:
-        finishModule g, m
-
   # Write C files
   if g.backend != nil:
     cgenWriteModules(g.backend, g.config)