diff --git a/Cargo.lock b/Cargo.lock
index 118837a2..2049508d 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -26,7 +26,7 @@ dependencies = [
 [[package]]
 name = "air"
 version = "0.3.0"
-source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#eeb6404188e4b4c9207b9e8e8a2120156602d92e"
+source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#bd8a91199f45fcb3c21af056468340e2f9de2d1d"
 dependencies = [
  "p3-field",
 ]
@@ -99,7 +99,7 @@ checksum = "c08606f8c3cbf4ce6ec8e28fb0014a2c086708fe954eaa885384a6165172e7e8"
 [[package]]
 name = "backend"
 version = "0.3.0"
-source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#eeb6404188e4b4c9207b9e8e8a2120156602d92e"
+source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#bd8a91199f45fcb3c21af056468340e2f9de2d1d"
 dependencies = [
  "itertools",
  "p3-field",
@@ -134,9 +134,9 @@ checksum = "9330f8b2ff13f34540b44e946ef35111825727b38d33286ef986142615121801"
 
 [[package]]
 name = "clap"
-version = "4.5.54"
+version = "4.5.56"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c6e6ff9dcd79cff5cd969a17a545d79e84ab086e444102a591e288a8aa3ce394"
+checksum = "a75ca66430e33a14957acc24c5077b503e7d374151b2b4b3a10c83b4ceb4be0e"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -144,9 +144,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.54"
+version = "4.5.56"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fa42cf4d2b7a41bc8f663a7cab4031ebafa1bf3875705bfaf8466dc60ab52c00"
+checksum = "793207c7fa6300a0608d1080b858e5fdbe713cdc1c8db9fb17777d8a13e63df0"
 dependencies = [
  "anstream",
  "anstyle",
@@ -156,9 +156,9 @@ dependencies = [
 
 [[package]]
 name = "clap_derive"
-version = "4.5.49"
+version = "4.5.55"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2a0b5487afeab2deb2ff4e03a807ad1a03ac532ff5a2cee5d86884440c7f7671"
+checksum = "a92793da1a46a5f2a02a6f4c46c6496b28c43638adea8306fcb0caa1634f24e5"
 dependencies = [
  "heck",
  "proc-macro2",
@@ -190,7 +190,7 @@ dependencies = [
 [[package]]
 name = "constraints-folder"
 version = "0.3.0"
-source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#eeb6404188e4b4c9207b9e8e8a2120156602d92e"
+source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#bd8a91199f45fcb3c21af056468340e2f9de2d1d"
 dependencies = [
  "air 0.3.0",
  "backend",
@@ -265,10 +265,12 @@ checksum = "877a4ace8713b0bcf2a4e7eec82529c029f1d0619886d18145fea96c3ffe5c0f"
 
 [[package]]
 name = "fiat-shamir"
-version = "0.1.0"
-source = "git+https://github.com/leanEthereum/fiat-shamir.git#493be07bdd8669a816d28c3befc08bc3e68e590a"
+version = "0.3.0"
+source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#bd8a91199f45fcb3c21af056468340e2f9de2d1d"
 dependencies = [
  "p3-field",
+ "p3-koala-bear",
+ "p3-poseidon2",
  "p3-symmetric",
  "rayon",
  "serde",
@@ -367,7 +369,6 @@ dependencies = [
  "rec_aggregation",
  "sub_protocols",
  "utils",
- "whir-p3",
  "xmss",
 ]
 
@@ -388,7 +389,6 @@ dependencies = [
  "sub_protocols",
  "tracing",
  "utils",
- "whir-p3",
  "xmss",
 ]
 
@@ -411,7 +411,6 @@ dependencies = [
  "sub_protocols",
  "tracing",
  "utils",
- "whir-p3",
  "witness_generation",
  "xmss",
 ]
@@ -436,7 +435,6 @@ dependencies = [
  "thiserror",
  "tracing",
  "utils",
- "whir-p3",
  "xmss",
 ]
 
@@ -470,17 +468,19 @@ checksum = "f52b00d39961fc5b2736ea853c9cc86238e165017a493d1d5c8eac6bdc4cc273"
 [[package]]
 name = "multilinear-toolkit"
 version = "0.3.0"
-source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#eeb6404188e4b4c9207b9e8e8a2120156602d92e"
+source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#bd8a91199f45fcb3c21af056468340e2f9de2d1d"
 dependencies = [
  "air 0.3.0",
  "backend",
  "constraints-folder",
  "fiat-shamir",
  "p3-field",
+ "p3-maybe-rayon",
  "p3-util",
  "rayon",
  "sumcheck",
  "tracing",
+ "whir",
 ]
 
 [[package]]
@@ -554,19 +554,6 @@ version = "1.70.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "384b8ab6d37215f3c5301a95a4accb5d64aa607f1fcb26a11b5303878451b4fe"
 
-[[package]]
-name = "p3-baby-bear"
-version = "0.3.0"
-source = "git+https://github.com/TomWambsgans/Plonky3.git?branch=lean-multisig#1f5aca1d6845caec76fa25b00fae3ea4f07ef930"
-dependencies = [
- "p3-field",
- "p3-mds",
- "p3-monty-31",
- "p3-poseidon2",
- "p3-symmetric",
- "rand",
-]
-
 [[package]]
 name = "p3-challenger"
 version = "0.3.0"
@@ -621,17 +608,6 @@ dependencies = [
  "tracing",
 ]
 
-[[package]]
-name = "p3-interpolation"
-version = "0.3.0"
-source = "git+https://github.com/TomWambsgans/Plonky3.git?branch=lean-multisig#1f5aca1d6845caec76fa25b00fae3ea4f07ef930"
-dependencies = [
- "p3-field",
- "p3-matrix",
- "p3-maybe-rayon",
- "p3-util",
-]
-
 [[package]]
 name = "p3-koala-bear"
 version = "0.3.0"
@@ -919,7 +895,6 @@ dependencies = [
  "sub_protocols",
  "tracing",
  "utils",
- "whir-p3",
  "xmss",
 ]
 
@@ -1069,13 +1044,12 @@ dependencies = [
  "rand",
  "tracing",
  "utils",
- "whir-p3",
 ]
 
 [[package]]
 name = "sumcheck"
 version = "0.3.0"
-source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#eeb6404188e4b4c9207b9e8e8a2120156602d92e"
+source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#bd8a91199f45fcb3c21af056468340e2f9de2d1d"
 dependencies = [
  "air 0.3.0",
  "backend",
@@ -1301,28 +1275,25 @@ dependencies = [
 ]
 
 [[package]]
-name = "whir-p3"
-version = "0.1.0"
-source = "git+https://github.com/TomWambsgans/whir-p3?branch=lean-multisig#bc7bf99c224d63582945f065f555b9824d843d3c"
+name = "whir"
+version = "0.3.0"
+source = "git+https://github.com/leanEthereum/multilinear-toolkit.git#bd8a91199f45fcb3c21af056468340e2f9de2d1d"
 dependencies = [
+ "backend",
+ "fiat-shamir",
  "itertools",
- "multilinear-toolkit",
- "p3-baby-bear",
  "p3-commit",
  "p3-dft",
  "p3-field",
- "p3-interpolation",
  "p3-koala-bear",
  "p3-matrix",
- "p3-maybe-rayon",
  "p3-merkle-tree",
  "p3-symmetric",
  "p3-util",
  "rand",
  "rayon",
+ "sumcheck",
  "tracing",
- "tracing-forest",
- "tracing-subscriber",
 ]
 
 [[package]]
@@ -1396,7 +1367,6 @@ dependencies = [
  "sub_protocols",
  "tracing",
  "utils",
- "whir-p3",
  "xmss",
 ]
 
@@ -1414,18 +1384,18 @@ dependencies = [
 
 [[package]]
 name = "zerocopy"
-version = "0.8.34"
+version = "0.8.37"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "71ddd76bcebeed25db614f82bf31a9f4222d3fbba300e6fb6c00afa26cbd4d9d"
+checksum = "7456cf00f0685ad319c5b1693f291a650eaf345e941d082fc4e03df8a03996ac"
 dependencies = [
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.8.34"
+version = "0.8.37"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d8187381b52e32220d50b255276aa16a084ec0a9017a0ca2152a1f55c539758d"
+checksum = "1328722bbf2115db7e19d69ebcc15e795719e2d66b60827c6a69a117365e37a0"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1434,6 +1404,6 @@ dependencies = [
 
 [[package]]
 name = "zmij"
-version = "1.0.17"
+version = "1.0.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02aae0f83f69aafc94776e879363e9771d7ecbffe2c7fbb6c14c5e00dfe88439"
+checksum = "1966f8ac2c1f76987d69a74d0e0f929241c10e78136434e3be70ff7f58f64214"
diff --git a/Cargo.toml b/Cargo.toml
index bc37a467..9e8d3fd1 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -78,8 +78,8 @@ p3-goldilocks = { git = "https://github.com/TomWambsgans/Plonky3.git", branch =
 p3-util = { git = "https://github.com/TomWambsgans/Plonky3.git", branch = "lean-multisig" }
 p3-monty-31 = { git = "https://github.com/TomWambsgans/Plonky3.git", branch = "lean-multisig" }
 
-whir-p3 = { git = "https://github.com/TomWambsgans/whir-p3", branch = "lean-multisig" }
 multilinear-toolkit = { git = "https://github.com/leanEthereum/multilinear-toolkit.git" }
+
 [dependencies]
 clap.workspace = true
 rec_aggregation.workspace = true
@@ -91,7 +91,6 @@ utils.workspace = true
 p3-koala-bear.workspace = true
 lean_vm.workspace = true
 multilinear-toolkit.workspace = true
-whir-p3.workspace = true
 
 [profile.release]
 lto = "thin"
diff --git a/README.md b/README.md
index 2e171dcd..cda2c3c7 100644
--- a/README.md
+++ b/README.md
@@ -43,7 +43,7 @@ To reproduce:
 
 ### Proof size
 
-WHIR intial rate = 1/4. Proof size ≈ 380 KiB. TODO: Merkle pruning + WHIR batch opening -> 256 KiB. (To go below 256 KiB -> rate 1/8 or 1/16 in the final recursion).
+WHIR intial rate = 1/4. Proof size ≈ 325 KiB. TODO: WHIR batch opening + [2024/108](https://eprint.iacr.org/2024/108.pdf) section 3.1  -> close to 256 KiB. (To go below 256 KiB -> rate 1/8 or 1/16 in the final recursion).
 
 ## Credits
 
diff --git a/crates/lean_compiler/Cargo.toml b/crates/lean_compiler/Cargo.toml
index e33b21b2..506d006e 100644
--- a/crates/lean_compiler/Cargo.toml
+++ b/crates/lean_compiler/Cargo.toml
@@ -16,7 +16,6 @@ p3-poseidon2.workspace = true
 p3-koala-bear.workspace = true
 p3-symmetric.workspace = true
 p3-util.workspace = true
-whir-p3.workspace = true
 tracing.workspace = true
 air.workspace = true
 sub_protocols.workspace = true
diff --git a/crates/lean_prover/Cargo.toml b/crates/lean_prover/Cargo.toml
index ed4593e7..caf9d445 100644
--- a/crates/lean_prover/Cargo.toml
+++ b/crates/lean_prover/Cargo.toml
@@ -16,7 +16,6 @@ p3-poseidon2.workspace = true
 p3-koala-bear.workspace = true
 p3-symmetric.workspace = true
 p3-util.workspace = true
-whir-p3.workspace = true
 tracing.workspace = true
 air.workspace = true
 sub_protocols.workspace = true
diff --git a/crates/lean_prover/src/common.rs b/crates/lean_prover/src/common.rs
index b196fde7..411cf433 100644
--- a/crates/lean_prover/src/common.rs
+++ b/crates/lean_prover/src/common.rs
@@ -1,6 +1,5 @@
 use crate::*;
 use lean_vm::*;
-use multilinear_toolkit::prelude::*;
 
 pub(crate) fn fold_bytecode(bytecode: &Bytecode, folding_challenges: &MultilinearPoint<EF>) -> Vec<EF> {
     let encoded_bytecode = padd_with_zero_to_next_power_of_two(
diff --git a/crates/lean_prover/src/lib.rs b/crates/lean_prover/src/lib.rs
index e14d05bb..92339a1c 100644
--- a/crates/lean_prover/src/lib.rs
+++ b/crates/lean_prover/src/lib.rs
@@ -1,10 +1,10 @@
 #![cfg_attr(not(test), allow(unused_crate_dependencies))]
 
 use lean_vm::{EF, F};
+use multilinear_toolkit::prelude::*;
 use utils::*;
 
 use lean_vm::execute_bytecode;
-use whir_p3::{FoldingFactor, SecurityAssumption, WhirConfigBuilder};
 use witness_generation::*;
 
 mod common;
diff --git a/crates/lean_prover/src/prove_execution.rs b/crates/lean_prover/src/prove_execution.rs
index 12da4c96..5ef4f698 100644
--- a/crates/lean_prover/src/prove_execution.rs
+++ b/crates/lean_prover/src/prove_execution.rs
@@ -4,13 +4,11 @@ use crate::common::*;
 use crate::*;
 use air::prove_air;
 use lean_vm::*;
-use multilinear_toolkit::prelude::*;
 
 use p3_util::log2_ceil_usize;
 use sub_protocols::*;
 use tracing::info_span;
 use utils::{build_prover_state, padd_with_zero_to_next_power_of_two};
-use whir_p3::{SparseStatement, SparseValue, WhirConfig};
 use xmss::Poseidon16History;
 
 #[derive(Debug)]
@@ -219,9 +217,9 @@ pub fn prove_execution(
         bytecode_pushforward_commitment,
         &bytecode_pushforward.by_ref(),
     );
-    let proof_size_fe = prover_state.proof_size_fe();
+    let proof_size_fe = prover_state.pruned_proof().proof_size_fe();
     ExecutionProof {
-        proof: prover_state.into_proof(),
+        proof: prover_state.raw_proof(),
         proof_size_fe,
         exec_summary,
         first_whir_n_vars,
diff --git a/crates/lean_prover/src/verify_execution.rs b/crates/lean_prover/src/verify_execution.rs
index e5a0ac17..e2d227b9 100644
--- a/crates/lean_prover/src/verify_execution.rs
+++ b/crates/lean_prover/src/verify_execution.rs
@@ -4,12 +4,10 @@ use crate::*;
 use crate::{SnarkParams, common::*};
 use air::verify_air;
 use lean_vm::*;
-use multilinear_toolkit::prelude::*;
 use p3_util::{log2_ceil_usize, log2_strict_usize};
 use sub_protocols::verify_logup_star;
 use sub_protocols::*;
 use utils::ToUsize;
-use whir_p3::{SparseStatement, SparseValue, WhirConfig};
 
 #[derive(Debug, Clone)]
 pub struct ProofVerificationDetails {
diff --git a/crates/lean_prover/witness_generation/Cargo.toml b/crates/lean_prover/witness_generation/Cargo.toml
index 01cfdb45..714476e9 100644
--- a/crates/lean_prover/witness_generation/Cargo.toml
+++ b/crates/lean_prover/witness_generation/Cargo.toml
@@ -16,7 +16,6 @@ p3-poseidon2.workspace = true
 p3-koala-bear.workspace = true
 p3-symmetric.workspace = true
 p3-util.workspace = true
-whir-p3.workspace = true
 tracing.workspace = true
 air.workspace = true
 sub_protocols.workspace = true
diff --git a/crates/lean_vm/Cargo.toml b/crates/lean_vm/Cargo.toml
index 1f3b9bf3..bc61e2ad 100644
--- a/crates/lean_vm/Cargo.toml
+++ b/crates/lean_vm/Cargo.toml
@@ -17,7 +17,6 @@ p3-poseidon2.workspace = true
 p3-koala-bear.workspace = true
 p3-symmetric.workspace = true
 p3-util.workspace = true
-whir-p3.workspace = true
 tracing.workspace = true
 air.workspace = true
 thiserror.workspace = true
diff --git a/crates/rec_aggregation/Cargo.toml b/crates/rec_aggregation/Cargo.toml
index 07c2dbd4..5db55cfc 100644
--- a/crates/rec_aggregation/Cargo.toml
+++ b/crates/rec_aggregation/Cargo.toml
@@ -14,7 +14,6 @@ p3-poseidon2.workspace = true
 p3-koala-bear.workspace = true
 p3-symmetric.workspace = true
 p3-util.workspace = true
-whir-p3.workspace = true
 tracing.workspace = true
 air.workspace = true
 sub_protocols.workspace = true
diff --git a/crates/rec_aggregation/src/recursion.rs b/crates/rec_aggregation/src/recursion.rs
index 0f4aabdb..bd2b90b8 100644
--- a/crates/rec_aggregation/src/recursion.rs
+++ b/crates/rec_aggregation/src/recursion.rs
@@ -13,7 +13,6 @@ use multilinear_toolkit::prelude::symbolic::{
 };
 use multilinear_toolkit::prelude::*;
 use utils::{Counter, MEMORY_TABLE_INDEX};
-use whir_p3::{WhirConfig, precompute_dft_twiddles};
 
 pub fn run_recursion_benchmark(count: usize, tracing: bool) {
     if tracing {
@@ -341,7 +340,7 @@ def main():
     );
     println!("{}", recursion_proof.exec_summary);
     println!(
-        "{}->1 recursion proving time: {} ms (1->1: {} ms), proof size: {} KiB (not optimized)",
+        "{}->1 recursion proving time: {} ms (1->1: {} ms), proof size: {} KiB",
         count,
         proving_time.as_millis(),
         proving_time.as_millis() / count as u128,
diff --git a/crates/rec_aggregation/src/xmss_aggregate.rs b/crates/rec_aggregation/src/xmss_aggregate.rs
index 7dbacea9..c26070d0 100644
--- a/crates/rec_aggregation/src/xmss_aggregate.rs
+++ b/crates/rec_aggregation/src/xmss_aggregate.rs
@@ -8,7 +8,6 @@ use std::sync::OnceLock;
 use std::time::Instant;
 use tracing::{info_span, instrument};
 use utils::to_little_endian_in_field;
-use whir_p3::precompute_dft_twiddles;
 use xmss::{
     Poseidon16History, V, XMSS_MAX_LOG_LIFETIME, XmssPublicKey, XmssSignature, xmss_generate_phony_signatures,
     xmss_verify_with_poseidon_trace,
@@ -97,7 +96,7 @@ pub fn run_xmss_benchmark(log_lifetimes: &[usize], tracing: bool) {
 
     println!("{summary}");
     println!(
-        "XMSS aggregation, proving time: {:.3} s ({:.1} XMSS/s), proof size: {} KiB (not optimized)",
+        "XMSS aggregation, proving time: {:.3} s ({:.1} XMSS/s), proof size: {} KiB",
         proving_time.as_secs_f64(),
         log_lifetimes.len() as f64 / proving_time.as_secs_f64(),
         n_field_elements_in_proof * F::bits() / (8 * 1024)
diff --git a/crates/sub_protocols/Cargo.toml b/crates/sub_protocols/Cargo.toml
index 51d8314d..bc353456 100644
--- a/crates/sub_protocols/Cargo.toml
+++ b/crates/sub_protocols/Cargo.toml
@@ -9,7 +9,6 @@ workspace = true
 [dependencies]
 tracing.workspace = true
 utils.workspace = true
-whir-p3.workspace = true
 p3-util.workspace = true
 lean_vm.workspace = true
 multilinear-toolkit.workspace = true
diff --git a/crates/sub_protocols/src/packed_pcs.rs b/crates/sub_protocols/src/packed_pcs.rs
index b8919ee0..68c7c47b 100644
--- a/crates/sub_protocols/src/packed_pcs.rs
+++ b/crates/sub_protocols/src/packed_pcs.rs
@@ -5,7 +5,6 @@ use p3_util::log2_ceil_usize;
 use std::collections::BTreeMap;
 use tracing::instrument;
 use utils::{VarCount, transpose_slice_to_basis_coefficients};
-use whir_p3::*;
 
 #[derive(Debug)]
 pub struct MultiCommitmentWitness {
diff --git a/crates/utils/src/wrappers.rs b/crates/utils/src/wrappers.rs
index 0c2aca6d..37e0dd9f 100644
--- a/crates/utils/src/wrappers.rs
+++ b/crates/utils/src/wrappers.rs
@@ -15,7 +15,7 @@ pub fn build_prover_state() -> ProverState<QuinticExtensionFieldKB, Poseidon16>
 pub fn build_verifier_state(
     prover_state: ProverState<QuinticExtensionFieldKB, Poseidon16>,
 ) -> VerifierState<QuinticExtensionFieldKB, Poseidon16> {
-    let mut verifier_state = VerifierState::new(prover_state.into_proof(), get_poseidon16().clone());
+    let mut verifier_state = VerifierState::new(prover_state.raw_proof(), get_poseidon16().clone());
     verifier_state.duplexing();
     verifier_state
 }
diff --git a/src/lib.rs b/src/lib.rs
index 042356e0..78ee4d3c 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -1,3 +1,4 @@
+use multilinear_toolkit::prelude::*;
 pub use multilinear_toolkit::prelude::{
     PrimeCharacteristicRing, // to allow `F::from_usize`
     ProofError,
@@ -17,7 +18,7 @@ pub use xmss::{
 
 pub fn xmss_aggregation_setup_prover() {
     rec_aggregation::xmss_aggregate::xmss_setup_aggregation_program();
-    whir_p3::precompute_dft_twiddles::<F>(1 << 24);
+    precompute_dft_twiddles::<F>(1 << 24);
 }
 
 pub fn xmss_aggregation_setup_verifier() {
diff --git a/src/prove_poseidons.rs b/src/prove_poseidons.rs
index 87a6aafc..714a3010 100644
--- a/src/prove_poseidons.rs
+++ b/src/prove_poseidons.rs
@@ -9,7 +9,6 @@ use rand::{Rng, SeedableRng, rngs::StdRng};
 use utils::{
     build_prover_state, build_verifier_state, collect_refs, init_tracing, padd_with_zero_to_next_power_of_two,
 };
-use whir_p3::{FoldingFactor, SecurityAssumption, SparseStatement, WhirConfig, WhirConfigBuilder};
 
 const WIDTH: usize = 16;
 const UNIVARIATE_SKIPS: usize = 3;