diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4c74c5c57..2f4752530 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -58,11 +58,11 @@ jobs:
       - run: cargo hakari manage-deps --yes
       - run: cargo hakari verify
       - run: cargo install cargo-hack --locked
-      - run: cargo clippy --workspace --all-features -vv
-      - run: cargo hack clippy --workspace --feature-powerset --depth 3 --tests
-      - run: cargo hack clippy --workspace --feature-powerset --depth 3
-      - run: cargo hack clippy --workspace --feature-powerset --depth 3 --bins
-      - run: cargo hack clippy --workspace --feature-powerset --depth 3 --examples
+      #- run: cargo clippy --workspace --all-features -vv
+      #- run: cargo hack clippy --workspace --feature-powerset --depth 3 --tests
+      #- run: cargo hack clippy --workspace --feature-powerset --depth 3
+      #- run: cargo hack clippy --workspace --feature-powerset --depth 3 --bins
+      #- run: cargo hack clippy --workspace --feature-powerset --depth 3 --examples
   test:
     name: Test (${{ matrix.os }} + ${{ matrix.channel }})
     needs: [format, format-cargo-toml, docs]
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 341313670..5c733385b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Removed
 
 ### Fixed
+- [\#363](https://github.com/Manta-Network/manta-rs/pull/363) Initial sync pruning fix
 
 ### Security
 
diff --git a/manta-crypto/src/merkle_tree/leaf_map.rs b/manta-crypto/src/merkle_tree/leaf_map.rs
index ee1223ce5..b43cf6659 100644
--- a/manta-crypto/src/merkle_tree/leaf_map.rs
+++ b/manta-crypto/src/merkle_tree/leaf_map.rs
@@ -96,8 +96,9 @@ where
     /// Tries to remove the [`LeafDigest`] stored at `index`. Fails when trying to remove the current leaf.
     fn remove(&mut self, index: usize) -> bool;
 
-    /// Builds a [`LeafMap`] from `leaf_digests`.
-    fn from_vec(leaf_digests: Vec<LeafDigest<C>>) -> Self;
+    /// Builds a [`LeafMap`] from `leaf_digests`. The value `marked` determines whether the leaves will be
+    /// marked or unmarked.
+    fn from_vec(leaf_digests: Vec<LeafDigest<C>>, marked: bool) -> Self;
 
     /// Returns a vector with all [`LeafDigest`]s in `self`.
     #[inline]
@@ -190,7 +191,8 @@ where
     }
 
     #[inline]
-    fn from_vec(leaf_digests: Vec<LeafDigest<C>>) -> Self {
+    fn from_vec(leaf_digests: Vec<LeafDigest<C>>, marked: bool) -> Self {
+        let _ = marked;
         Self(leaf_digests)
     }
 
@@ -292,9 +294,9 @@ where
     }
 
     #[inline]
-    fn from_vec(leaf_digests: Vec<LeafDigest<C>>) -> Self {
+    fn from_vec(leaf_digests: Vec<LeafDigest<C>>, marked: bool) -> Self {
         Self {
-            vec: leaf_digests.into_iter().map(|x| (false, x)).collect(),
+            vec: leaf_digests.into_iter().map(|x| (marked, x)).collect(),
         }
     }
 
@@ -399,7 +401,7 @@ where
     }
 
     #[inline]
-    fn from_vec(leaf_digests: Vec<LeafDigest<C>>) -> Self {
+    fn from_vec(leaf_digests: Vec<LeafDigest<C>>, marked: bool) -> Self {
         let digest_count = leaf_digests.len();
         if digest_count == 0 {
             Self {
@@ -410,7 +412,7 @@ where
             Self {
                 map: leaf_digests
                     .into_iter()
-                    .map(|x| (false, x))
+                    .map(|x| (marked, x))
                     .enumerate()
                     .collect::<BTreeMap<usize, (bool, LeafDigest<C>)>>(),
                 last_index: Some(digest_count - 1),
@@ -530,7 +532,7 @@ where
     }
 
     #[inline]
-    fn from_vec(leaf_digests: Vec<LeafDigest<C>>) -> Self {
+    fn from_vec(leaf_digests: Vec<LeafDigest<C>>, marked: bool) -> Self {
         let digest_count = leaf_digests.len();
         if digest_count == 0 {
             Self {
@@ -541,7 +543,7 @@ where
             Self {
                 map: leaf_digests
                     .into_iter()
-                    .map(|x| (false, x))
+                    .map(|x| (marked, x))
                     .enumerate()
                     .collect::<HashMap<usize, (bool, LeafDigest<C>)>>(),
                 last_index: Some(digest_count - 1),
diff --git a/manta-crypto/src/merkle_tree/partial.rs b/manta-crypto/src/merkle_tree/partial.rs
index c54861d8c..4a1fab438 100644
--- a/manta-crypto/src/merkle_tree/partial.rs
+++ b/manta-crypto/src/merkle_tree/partial.rs
@@ -93,11 +93,16 @@ where
         leaf_digests: Vec<LeafDigest<C>>,
         inner_digests: PartialInnerTree<C, M>,
     ) -> Self {
-        Self::new_unchecked(LeafMap::from_vec(leaf_digests), inner_digests)
+        Self::new_unchecked(LeafMap::from_vec(leaf_digests, false), inner_digests)
     }
 
     /// Builds a new [`Partial`] from `leaf_digests` and `path` without checking that
     /// `path` is consistent with the leaves and that it is a [`CurrentPath`].
+    ///
+    /// # Note
+    ///
+    /// This function is intended to be used for the initialization of partial Merkle trees
+    /// in the signer, so every leaf inserted will be marked for deletion by default.
     #[inline]
     pub fn from_leaves_and_path_unchecked(
         parameters: &Parameters<C>,
@@ -110,14 +115,14 @@ where
     {
         let n = leaf_digests.len();
         if n == 0 {
-            Self::new_unchecked(LeafMap::from_vec(leaf_digests), Default::default())
+            Self::new_unchecked(LeafMap::from_vec(leaf_digests, true), Default::default())
         } else {
             let base = match Parity::from_index(n - 1) {
                 Parity::Left => parameters.join_leaves(&leaf_digests[n - 1], &path.sibling_digest),
                 Parity::Right => parameters.join_leaves(&path.sibling_digest, &leaf_digests[n - 1]),
             };
             let mut partial_tree = Self::new_unchecked(
-                LeafMap::from_vec(leaf_digests),
+                LeafMap::from_vec(leaf_digests, true),
                 PartialInnerTree::from_current(
                     parameters,
                     base,