diff --git a/compiler/src/iree/compiler/Pipelines/Options.cpp b/compiler/src/iree/compiler/Pipelines/Options.cpp
index 83e0bec..5257479 100644
--- a/compiler/src/iree/compiler/Pipelines/Options.cpp
+++ b/compiler/src/iree/compiler/Pipelines/Options.cpp
@@ -91,18 +91,6 @@
       llvm::cl::desc(
           "File name of a transform dialect spec to use for preprocessing."),
       llvm::cl::cat(category));
-
-  // DEPRECATED: do not add explicit options for specific passes.
-  binder.opt<TransposeMatmulInput>(
-      "iree-preprocessing-transpose-matmul", preprocessingTransposeMatmulInput,
-      llvm::cl::desc("Convert Linalg matmul ops to transposed variants."),
-      llvm::cl::cat(category),
-      llvm::cl::values(clEnumValN(TransposeMatmulInput::Lhs, "lhs",
-                                  "Transpose LHS input matrix."),
-                       clEnumValN(TransposeMatmulInput::Rhs, "rhs",
-                                  "Transpose RHS input matrix."),
-                       clEnumValN(TransposeMatmulInput::None, "none",
-                                  "Transpose neither input (disable).")));
 }
 
 void GlobalOptimizationOptions::bindOptions(OptionsBinder &binder) {
diff --git a/compiler/src/iree/compiler/Pipelines/Options.h b/compiler/src/iree/compiler/Pipelines/Options.h
index b704599..5fdec6e 100644
--- a/compiler/src/iree/compiler/Pipelines/Options.h
+++ b/compiler/src/iree/compiler/Pipelines/Options.h
@@ -68,19 +68,6 @@
   std::string preprocessingTransformSpecFilename;
   std::string preprocessingPDLSpecFilename;
 
-  // DEPRECATED: do not put pass-specific options here and instead use the
-  // pass pipeline.
-  enum class TransposeMatmulInput {
-    /// Transpose LHS input matrix.
-    Lhs,
-    /// Transpose RHS input matrix.
-    Rhs,
-    /// Transpose neither input (disable).
-    None
-  };
-  TransposeMatmulInput preprocessingTransposeMatmulInput =
-      TransposeMatmulInput::None;
-
   void bindOptions(OptionsBinder &binder);
   using FromFlags = OptionsFromFlags<PreprocessingOptions>;
 };
diff --git a/compiler/src/iree/compiler/Preprocessing/Common/BUILD.bazel b/compiler/src/iree/compiler/Preprocessing/Common/BUILD.bazel
index 5df1f31..e004a55 100644
--- a/compiler/src/iree/compiler/Preprocessing/Common/BUILD.bazel
+++ b/compiler/src/iree/compiler/Preprocessing/Common/BUILD.bazel
@@ -55,7 +55,6 @@
         "//compiler/src/iree/compiler/Dialect/HAL/IR",
         "//compiler/src/iree/compiler/Dialect/Stream/IR",
         "//compiler/src/iree/compiler/Dialect/Util/IR",
-        "//compiler/src/iree/compiler/Pipelines:Options",
         "@llvm-project//llvm:Support",
         "@llvm-project//mlir:AffineDialect",
         "@llvm-project//mlir:ArithDialect",
diff --git a/compiler/src/iree/compiler/Preprocessing/Common/CMakeLists.txt b/compiler/src/iree/compiler/Preprocessing/Common/CMakeLists.txt
index 6f1fbcb..c9c127c 100644
--- a/compiler/src/iree/compiler/Preprocessing/Common/CMakeLists.txt
+++ b/compiler/src/iree/compiler/Preprocessing/Common/CMakeLists.txt
@@ -66,7 +66,6 @@
     iree::compiler::Dialect::HAL::IR
     iree::compiler::Dialect::Stream::IR
     iree::compiler::Dialect::Util::IR
-    iree::compiler::Pipelines::Options
   PUBLIC
 )
 
diff --git a/compiler/src/iree/compiler/Preprocessing/Common/Passes.h b/compiler/src/iree/compiler/Preprocessing/Common/Passes.h
index 5f8fb11..937d644 100644
--- a/compiler/src/iree/compiler/Preprocessing/Common/Passes.h
+++ b/compiler/src/iree/compiler/Preprocessing/Common/Passes.h
@@ -9,7 +9,6 @@
 
 #include <functional>
 
-#include "iree/compiler/Pipelines/Options.h"
 #include "mlir/Interfaces/FunctionInterfaces.h"
 #include "mlir/Pass/Pass.h"
 #include "mlir/Pass/PassManager.h"
@@ -26,6 +25,15 @@
   All = 2,
 };
 
+enum class TransposeMatmulInput {
+  /// Transpose LHS input matrix.
+  Lhs,
+  /// Transpose RHS input matrix.
+  Rhs,
+  /// Transpose neither input (disable).
+  None
+};
+
 //===----------------------------------------------------------------------===//
 // Register all Passes
 //===----------------------------------------------------------------------===//
diff --git a/compiler/src/iree/compiler/Preprocessing/Common/Passes.td b/compiler/src/iree/compiler/Preprocessing/Common/Passes.td
index c04e2bf..4e562a7 100644
--- a/compiler/src/iree/compiler/Preprocessing/Common/Passes.td
+++ b/compiler/src/iree/compiler/Preprocessing/Common/Passes.td
@@ -116,15 +116,15 @@
 def TransposeMatmulPass : Pass<"iree-preprocessing-transpose-matmul-pass"> {
   let summary = "Convert Linalg matmul ops to transposed variants";
   let options = [
-    Option<"input", "input", "PreprocessingOptions::TransposeMatmulInput",
-           /*default=*/"PreprocessingOptions::TransposeMatmulInput::None",
+    Option<"input", "input", "Preprocessing::TransposeMatmulInput",
+           /*default=*/"Preprocessing::TransposeMatmulInput::None",
            "Input to transpose, one of: 'none' (default), 'lhs', 'rhs'",
            [{llvm::cl::values(
-              clEnumValN(PreprocessingOptions::TransposeMatmulInput::Lhs, "lhs",
+              clEnumValN(Preprocessing::TransposeMatmulInput::Lhs, "lhs",
                          "Transpose LHS input matrix."),
-              clEnumValN(PreprocessingOptions::TransposeMatmulInput::Rhs, "rhs",
+              clEnumValN(Preprocessing::TransposeMatmulInput::Rhs, "rhs",
                          "Transpose RHS input matrix."),
-              clEnumValN(PreprocessingOptions::TransposeMatmulInput::None, "none",
+              clEnumValN(Preprocessing::TransposeMatmulInput::None, "none",
                          "Transpose neither input (disable)."))
            }]>
   ];
diff --git a/compiler/src/iree/compiler/Preprocessing/Common/TransposeMatmul.cpp b/compiler/src/iree/compiler/Preprocessing/Common/TransposeMatmul.cpp
index 26e9c05..b2c1244 100644
--- a/compiler/src/iree/compiler/Preprocessing/Common/TransposeMatmul.cpp
+++ b/compiler/src/iree/compiler/Preprocessing/Common/TransposeMatmul.cpp
@@ -4,7 +4,6 @@
 // See https://llvm.org/LICENSE.txt for license information.
 // SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
 
-#include "iree/compiler/Pipelines/Options.h"
 #include "iree/compiler/Preprocessing/Common/Passes.h"
 #include "mlir/Dialect/Linalg/IR/Linalg.h"
 #include "mlir/Dialect/Linalg/Transforms/Transforms.h"
@@ -22,11 +21,10 @@
       TransposeMatmulPass>::TransposeMatmulPassBase;
 
   void runOnOperation() override {
-    if (input == PreprocessingOptions::TransposeMatmulInput::None)
+    if (input == Preprocessing::TransposeMatmulInput::None)
       return;
 
-    bool transposeLHS =
-        input == PreprocessingOptions::TransposeMatmulInput::Lhs;
+    bool transposeLHS = input == Preprocessing::TransposeMatmulInput::Lhs;
 
     RewritePatternSet patterns(&getContext());
     linalg::populateTransposeMatmulPatterns(patterns, transposeLHS);
diff --git a/compiler/src/iree/compiler/Preprocessing/Passes.cpp b/compiler/src/iree/compiler/Preprocessing/Passes.cpp
index a81cac4..77f6da5 100644
--- a/compiler/src/iree/compiler/Preprocessing/Passes.cpp
+++ b/compiler/src/iree/compiler/Preprocessing/Passes.cpp
@@ -93,16 +93,6 @@
     passManager.addPass(createCanonicalizerPass());
     passManager.addPass(createCSEPass());
   }
-
-  // DEPRECATED: do not add explicit options for specific passes.
-  if (preprocessingOptions.preprocessingTransposeMatmulInput !=
-      PreprocessingOptions::TransposeMatmulInput::None) {
-    Preprocessing::TransposeMatmulPassOptions transposeMatmulOptions;
-    transposeMatmulOptions.input =
-        preprocessingOptions.preprocessingTransposeMatmulInput;
-    passManager.addPass(
-        Preprocessing::createTransposeMatmulPass(transposeMatmulOptions));
-  }
 }
 
 static void