diff --git a/provekit/common/Cargo.toml b/provekit/common/Cargo.toml
index 3acdbefc3..ad355845d 100644
--- a/provekit/common/Cargo.toml
+++ b/provekit/common/Cargo.toml
@@ -41,6 +41,7 @@ rayon.workspace = true
 ruint.workspace = true
 serde.workspace = true
 serde_json.workspace = true
+sha3.workspace = true
 tracing.workspace = true
 xz2.workspace = true
 zerocopy.workspace = true
diff --git a/provekit/common/src/r1cs.rs b/provekit/common/src/r1cs.rs
index c971d9f19..2e34bb006 100644
--- a/provekit/common/src/r1cs.rs
+++ b/provekit/common/src/r1cs.rs
@@ -4,6 +4,7 @@ use {
     },
     ark_ff::Zero,
     serde::{Deserialize, Serialize},
+    sha3::{Digest, Sha3_256},
     std::collections::HashMap,
 };
 
@@ -61,6 +62,12 @@ impl R1CS {
         self.a.num_cols
     }
 
+    #[must_use]
+    pub fn hash(&self) -> [u8; 32] {
+        let bytes = postcard::to_stdvec(self).expect("R1CS serialization failed");
+        Sha3_256::digest(&bytes).into()
+    }
+
     // Increase the size of the R1CS matrices to the specified dimensions.
     pub fn grow_matrices(&mut self, num_rows: usize, num_cols: usize) {
         self.a.grow(num_rows, num_cols);
diff --git a/provekit/common/src/whir_r1cs.rs b/provekit/common/src/whir_r1cs.rs
index e36713a5c..05c9714ff 100644
--- a/provekit/common/src/whir_r1cs.rs
+++ b/provekit/common/src/whir_r1cs.rs
@@ -27,6 +27,7 @@ pub struct WhirR1CSScheme {
     pub num_challenges:    usize,
     pub has_public_inputs: bool,
     pub whir_witness:      WhirZkConfig,
+    pub r1cs_hash:         [u8; 32],
 }
 
 impl WhirR1CSScheme {
diff --git a/provekit/common/src/witness/mod.rs b/provekit/common/src/witness/mod.rs
index f7cf80db2..858d244ae 100644
--- a/provekit/common/src/witness/mod.rs
+++ b/provekit/common/src/witness/mod.rs
@@ -10,7 +10,7 @@ use {
         utils::{serde_ark, serde_ark_vec},
         FieldElement,
     },
-    ark_ff::{BigInt, One, PrimeField},
+    ark_ff::{BigInt, BigInteger, One, PrimeField},
     serde::{Deserialize, Serialize},
 };
 pub use {
@@ -91,6 +91,16 @@ impl PublicInputs {
             _ => self.0.iter().copied().reduce(compress).unwrap(),
         }
     }
+
+    #[must_use]
+    pub fn hash_bytes(&self) -> [u8; 32] {
+        let hash = self.hash();
+        let bytes = hash.into_bigint().to_bytes_le();
+        let mut result = [0u8; 32];
+        let len = bytes.len().min(32);
+        result[..len].copy_from_slice(&bytes[..len]);
+        result
+    }
 }
 
 impl Default for PublicInputs {
diff --git a/provekit/prover/src/lib.rs b/provekit/prover/src/lib.rs
index bbac4de0a..fa80307df 100644
--- a/provekit/prover/src/lib.rs
+++ b/provekit/prover/src/lib.rs
@@ -5,7 +5,7 @@ use {
         r1cs::{CompressedLayers, CompressedR1CS},
         whir_r1cs::WhirR1CSProver,
     },
-    acir::native_types::WitnessMap,
+    acir::native_types::{Witness, WitnessMap},
     anyhow::{Context, Result},
     bn254_blackbox_solver::Bn254BlackBoxSolver,
     mavros_vm::interpreter as mavros_interpreter,
@@ -13,12 +13,12 @@ use {
     noir_artifact_cli::fs::inputs::read_inputs_from_file,
     noirc_abi::InputMap,
     provekit_common::{
-        FieldElement, MavrosProver, NoirElement, NoirProof, NoirProver, Prover, PublicInputs,
-        TranscriptSponge,
+        utils::noir_to_native, FieldElement, MavrosProver, NoirElement, NoirProof, NoirProver,
+        Prover, PublicInputs, TranscriptSponge,
     },
     std::{mem::size_of, path::Path},
     tracing::{debug, info_span, instrument},
-    whir::transcript::{codecs::Empty, ProverState, VerifierMessage},
+    whir::transcript::{ProverState, VerifierMessage},
 };
 
 pub mod input_utils;
@@ -69,7 +69,24 @@ impl Prove for NoirProver {
         provekit_common::register_ntt();
 
         let acir_witness_idx_to_value_map = generate_noir_witness(&mut self, input_map)?;
-        let num_public_inputs = self.program.functions[0].public_inputs().indices().len();
+
+        let mut public_input_indices = self.program.functions[0].public_inputs().indices();
+        public_input_indices.sort_unstable();
+        let public_inputs = if public_input_indices.is_empty() {
+            PublicInputs::new()
+        } else {
+            let values = public_input_indices
+                .iter()
+                .map(|&idx| {
+                    let noir_val = acir_witness_idx_to_value_map
+                        .get(&Witness::from(idx))
+                        .ok_or_else(|| anyhow::anyhow!("Missing public input at index {idx}"))?;
+                    Ok(noir_to_native(*noir_val))
+                })
+                .collect::<Result<Vec<_>>>()?;
+            PublicInputs::from_vec(values)
+        };
+
         drop(self.program);
         drop(self.witness_generator);
 
@@ -80,18 +97,17 @@ impl Prove for NoirProver {
         let num_witnesses = compressed_r1cs.num_witnesses();
         let num_constraints = compressed_r1cs.num_constraints();
 
-        // Set up transcript with sponge selected by hash_config.
+        // Set up transcript with public inputs bound to the instance.
+        let instance = public_inputs.hash_bytes();
         let ds = self
             .whir_for_witness
             .create_domain_separator()
-            .instance(&Empty);
+            .instance(&instance);
         let mut merlin = ProverState::new(&ds, TranscriptSponge::from_config(self.hash_config));
 
         let mut witness: Vec<Option<FieldElement>> = vec![None; num_witnesses];
 
         // Solve w1 (or all witnesses if no challenges).
-        // Outer span captures memory AFTER w1_layers parameter is freed
-        // (parameter drop happens before outer span close).
         {
             let _s = info_span!("solve_w1").entered();
             crate::r1cs::solve_witness_vec(
@@ -178,17 +194,6 @@ impl Prove for NoirProver {
         r1cs.test_witness_satisfaction(&witness.iter().map(|w| w.unwrap()).collect::<Vec<_>>())
             .context("While verifying R1CS instance")?;
 
-        let public_inputs = if num_public_inputs == 0 {
-            PublicInputs::new()
-        } else {
-            PublicInputs::from_vec(
-                witness[1..=num_public_inputs]
-                    .iter()
-                    .map(|w| w.ok_or_else(|| anyhow::anyhow!("Missing public input witness")))
-                    .collect::<Result<Vec<FieldElement>>>()?,
-            )
-        };
-
         let full_witness: Vec<FieldElement> = witness
             .into_iter()
             .enumerate()
@@ -227,10 +232,20 @@ impl Prove for MavrosProver {
             &params,
         );
 
+        let num_public_inputs = self.num_public_inputs;
+        let public_inputs = if num_public_inputs == 0 {
+            PublicInputs::new()
+        } else {
+            // TODO : Verify marvos prover's handling of public input
+            PublicInputs::from_vec(phase1.out_wit_pre_comm[1..=num_public_inputs].to_vec())
+        };
+
+        // Set up transcript with public inputs bound to the instance.
+        let instance = public_inputs.hash_bytes();
         let ds = self
             .whir_for_witness
             .create_domain_separator()
-            .instance(&Empty);
+            .instance(&instance);
         let mut merlin = ProverState::new(&ds, TranscriptSponge::from_config(self.hash_config));
 
         let commitment_1 = self
@@ -244,7 +259,7 @@ impl Prove for MavrosProver {
             )
             .context("While committing to w1")?;
 
-        let (commitments, witgen_result) = if self.whir_for_witness.num_challenges > 0 {
+        let commitments = if self.whir_for_witness.num_challenges > 0 {
             let challenges: Vec<FieldElement> = (0..self.witness_layout.challenges_size)
                 .map(|_| merlin.verifier_message())
                 .collect();
@@ -267,22 +282,15 @@ impl Prove for MavrosProver {
                 )
                 .context("While committing to w2")?;
 
-            (vec![commitment_1, commitment_2], witgen_result)
+            vec![commitment_1, commitment_2]
         } else {
-            let witgen_result = mavros_interpreter::run_phase2(
+            mavros_interpreter::run_phase2(
                 phase1.clone(),
                 &[],
                 self.witness_layout,
                 self.constraints_layout,
             );
-            (vec![commitment_1], witgen_result)
-        };
-
-        let num_public_inputs = self.num_public_inputs;
-        let public_inputs = if num_public_inputs == 0 {
-            PublicInputs::new()
-        } else {
-            PublicInputs::from_vec(witgen_result.out_wit_pre_comm[1..=num_public_inputs].to_vec())
+            vec![commitment_1]
         };
 
         let whir_r1cs_proof = self
diff --git a/provekit/r1cs-compiler/src/whir_r1cs.rs b/provekit/r1cs-compiler/src/whir_r1cs.rs
index 0b18b19f5..526a1022a 100644
--- a/provekit/r1cs-compiler/src/whir_r1cs.rs
+++ b/provekit/r1cs-compiler/src/whir_r1cs.rs
@@ -76,6 +76,7 @@ impl WhirR1CSSchemeBuilder for WhirR1CSScheme {
             num_challenges,
             whir_witness: Self::new_whir_zk_config_for_size(m_raw, 1, hash_id),
             has_public_inputs,
+            r1cs_hash: r1cs.hash(),
         }
     }
 
@@ -154,6 +155,7 @@ impl WhirR1CSSchemeBuilder for WhirR1CSScheme {
             w1_size,
             num_challenges,
             has_public_inputs,
+            r1cs_hash: [0u8; 32], // TODO: Mavros path needs r1cs_hash
         }
     }
 }
diff --git a/provekit/verifier/src/whir_r1cs.rs b/provekit/verifier/src/whir_r1cs.rs
index 59288172b..daabee7ec 100644
--- a/provekit/verifier/src/whir_r1cs.rs
+++ b/provekit/verifier/src/whir_r1cs.rs
@@ -14,7 +14,7 @@ use {
     tracing::instrument,
     whir::{
         algebra::linear_form::LinearForm,
-        transcript::{codecs::Empty, Proof, VerifierMessage, VerifierState},
+        transcript::{Proof, VerifierMessage, VerifierState},
     },
 };
 
@@ -44,7 +44,8 @@ impl WhirR1CSVerifier for WhirR1CSScheme {
         r1cs: &R1CS,
         hash_config: HashConfig,
     ) -> Result<()> {
-        let ds = self.create_domain_separator().instance(&Empty);
+        let instance = public_inputs.hash_bytes();
+        let ds = self.create_domain_separator().instance(&instance);
         let whir_proof = Proof {
             narg_string: proof.narg_string.clone(),
             hints: proof.hints.clone(),