diff --git a/flang/include/flang/Frontend/FrontendOptions.h b/flang/include/flang/Frontend/FrontendOptions.h
--- a/flang/include/flang/Frontend/FrontendOptions.h
+++ b/flang/include/flang/Frontend/FrontendOptions.h
@@ -104,10 +104,22 @@
   /// The kind of input, atm it contains language
   InputKind kind_;
 
+  /// Is this input file in fixed-form format? This is simply derived from the
+  /// file extension and should not be altered by consumers. For input from
+  /// stdin this is never modified.
+  bool isFixedForm_ = false;
+
 public:
   FrontendInputFile() = default;
   FrontendInputFile(llvm::StringRef file, InputKind kind)
-      : file_(file.str()), kind_(kind) {}
+      : file_(file.str()), kind_(kind) {
+
+    // Based on the extension, decide whether this is a fixed or free form
+    // file.
+    auto pathDotIndex{file.rfind(".")};
+    std::string pathSuffix{file.substr(pathDotIndex + 1)};
+    isFixedForm_ = isFixedFormSuffix(pathSuffix);
+  }
   FrontendInputFile(const llvm::MemoryBuffer *buffer, InputKind kind)
       : buffer_(buffer), kind_(kind) {}
 
@@ -116,6 +128,7 @@
   bool IsEmpty() const { return file_.empty() && buffer_ == nullptr; }
   bool IsFile() const { return !IsBuffer(); }
   bool IsBuffer() const { return buffer_ != nullptr; }
+  bool IsFixedForm() const { return isFixedForm_; }
 
   llvm::StringRef file() const {
     assert(IsFile());
diff --git a/flang/lib/Frontend/CompilerInstance.cpp b/flang/lib/Frontend/CompilerInstance.cpp
--- a/flang/lib/Frontend/CompilerInstance.cpp
+++ b/flang/lib/Frontend/CompilerInstance.cpp
@@ -138,16 +138,22 @@
 }
 
 bool CompilerInstance::ExecuteAction(FrontendAction &act) {
+  auto &invoc = this->invocation();
+
   // Set some sane defaults for the frontend.
-  // TODO: Instead of defaults we should be setting these options based on the
-  // user input.
-  this->invocation().SetDefaultFortranOpts();
-  // Set the fortran options to user-based input.
-  this->invocation().setFortranOpts();
+  invoc.SetDefaultFortranOpts();
+  // Update the fortran options based on user-based input.
+  invoc.setFortranOpts();
 
-  // Connect Input to a CompileInstance
+  // Run the frontend action `act` for every input file.
   for (const FrontendInputFile &fif : frontendOpts().inputs_) {
     if (act.BeginSourceFile(*this, fif)) {
+      // Switch between fixed and free form format based on the input file
+      // extension. Ideally we should have all Fortran options set before
+      // entering this loop (i.e. processing any input files). However, we
+      // can't decide between fixed and free form based on the file extension
+      // earlier than this.
+      invoc.fortranOpts().isFixedForm = fif.IsFixedForm();
       if (llvm::Error err = act.Execute()) {
         consumeError(std::move(err));
       }
diff --git a/flang/lib/Frontend/FrontendAction.cpp b/flang/lib/Frontend/FrontendAction.cpp
--- a/flang/lib/Frontend/FrontendAction.cpp
+++ b/flang/lib/Frontend/FrontendAction.cpp
@@ -53,12 +53,6 @@
 
   Fortran::parser::Options parserOptions =
       this->instance().invocation().fortranOpts();
-  // Set the fixed form flag based on the file extension
-  auto pathDotIndex{currentInputPath.rfind(".")};
-  if (pathDotIndex != std::string::npos) {
-    std::string pathSuffix{currentInputPath.substr(pathDotIndex + 1)};
-    parserOptions.isFixedForm = isFixedFormSuffix(pathSuffix);
-  }
 
   // Prescan. In case of failure, report and return.
   ci.parsing().Prescan(currentInputPath, parserOptions);