diff --git a/.github/workflows/ci-prover-e2e.yml b/.github/workflows/ci-prover-e2e.yml
index f5f2819b55e4..a1843ef9e2d3 100644
--- a/.github/workflows/ci-prover-e2e.yml
+++ b/.github/workflows/ci-prover-e2e.yml
@@ -43,10 +43,19 @@ jobs:
         run: |
           git fetch
           # Checkout the commit with the DualVerifier contract to test FFLONK interface
-          git checkout b4d5b984
+          git checkout b68a01afa494fbb2fe85c954f0afe0d36ef589ca
           git submodule update --init --recursive
           git rev-parse HEAD
 
+      - name: Set new genesis for fflonk 
+        # Note, that while `Verifier` is not explicitly a part of the genensis state,
+        # it affects it indirectly as it is a part of the repo.
+        working-directory: ./etc/env/file_based
+        if: matrix.compressor-mode == 'fflonk'
+        run: |
+          sudo sed -i 's/^genesis_root: .*/genesis_root: 0xc2cbb3df06a08ba40810e07848d6522f5def60d9206b3638ee60d72cd9fac83c/' genesis.yaml
+          sudo sed -i "s/^genesis_batch_commitment: .*/genesis_batch_commitment: 0x5edce2e6a07abbb54d71581905b8fa3d9b9ecafea9add94be3c1b8ae709e690a/" genesis.yaml
+
       - name: Init
         run: |
           ci_run chmod -R +x ./bin
diff --git a/core/lib/l1_contract_interface/src/i_executor/methods/prove_batches.rs b/core/lib/l1_contract_interface/src/i_executor/methods/prove_batches.rs
index 2d02bd5a1764..817448cc1b62 100644
--- a/core/lib/l1_contract_interface/src/i_executor/methods/prove_batches.rs
+++ b/core/lib/l1_contract_interface/src/i_executor/methods/prove_batches.rs
@@ -58,8 +58,10 @@ impl ProveBatches {
                 }
             };
 
+            let should_use_fflonk = !is_verifier_pre_fflonk || !protocol_version.is_pre_fflonk();
+
             if protocol_version.is_pre_gateway() {
-                let proof_input = if !is_verifier_pre_fflonk || !protocol_version.is_pre_fflonk() {
+                let proof_input = if should_use_fflonk {
                     Token::Tuple(vec![
                         Token::Array(vec![verifier_type.into_token()]),
                         Token::Array(proof.into_iter().map(Token::Uint).collect()),
@@ -73,7 +75,17 @@ impl ProveBatches {
 
                 vec![prev_l1_batch_info, batches_arg, proof_input]
             } else {
-                let proof_input = Token::Array(proof.into_iter().map(Token::Uint).collect());
+                let proof_input = if should_use_fflonk {
+                    Token::Array(
+                        vec![verifier_type]
+                            .into_iter()
+                            .chain(proof)
+                            .map(Token::Uint)
+                            .collect(),
+                    )
+                } else {
+                    Token::Array(proof.into_iter().map(Token::Uint).collect())
+                };
 
                 let encoded_data = encode(&[prev_l1_batch_info, batches_arg, proof_input]);
                 let prove_data = [[SUPPORTED_ENCODING_VERSION].to_vec(), encoded_data]