diff --git a/.github/workflows/ci.generate.ts b/.github/workflows/ci.generate.ts
index 021c184258..87fcecc96c 100755
--- a/.github/workflows/ci.generate.ts
+++ b/.github/workflows/ci.generate.ts
@@ -86,7 +86,7 @@ ${installPkgsCommand} || echo 'Failed. Trying again.' && sudo apt-get clean && s
 (yes '' | sudo update-alternatives --force --all) > /dev/null 2> /dev/null || true
 
 echo "Decompressing sysroot..."
-wget -q https://github.com/denoland/deno_sysroot_build/releases/download/sysroot-20240207/sysroot-\`uname -m\`.tar.xz -O /tmp/sysroot.tar.xz
+wget -q https://github.com/denoland/deno_sysroot_build/releases/download/sysroot-20240527/sysroot-\`uname -m\`.tar.xz -O /tmp/sysroot.tar.xz
 cd /
 xzcat /tmp/sysroot.tar.xz | sudo tar -x
 sudo mount --rbind /dev /sysroot/dev
@@ -95,21 +95,23 @@ sudo mount --rbind /home /sysroot/home
 sudo mount -t proc /proc /sysroot/proc
 cd
 
-if [[ \`uname -m\` == "aarch64" ]]; then
-  echo "Copying libdl.a"
-  sudo cp /sysroot/usr/lib/aarch64-linux-gnu/libdl.a /sysroot/lib/aarch64-linux-gnu/libdl.a
-  echo "Copying libdl.so"
-  sudo cp /sysroot/lib/aarch64-linux-gnu/libdl.so.2 /sysroot/lib/aarch64-linux-gnu/libdl.so
-else
-  echo "Copying libdl.a"
-  sudo cp /sysroot/usr/lib/x86_64-linux-gnu/libdl.a /sysroot/lib/x86_64-linux-gnu/libdl.a
-  echo "Copying libdl.so"
-  sudo cp /sysroot/lib/x86_64-linux-gnu/libdl.so.2 /sysroot/lib/x86_64-linux-gnu/libdl.so
-fi
+echo "Done."
 
 # Configure the build environment. Both Rust and Clang will produce
 # llvm bitcode only, so we can use lld's incremental LTO support.
-cat >> $GITHUB_ENV << __0
+
+# Load the sysroot's env vars
+echo "sysroot env:"
+cat /sysroot/.env
+. /sysroot/.env
+
+# Important notes:
+#   1. -ldl seems to be required to avoid a failure in FFI tests. This flag seems
+#      to be in the Rust default flags in the smoketest, so uncertain why we need
+#      to be explicit here.
+#   2. RUSTFLAGS and RUSTDOCFLAGS must be specified, otherwise the doctests fail
+#      to build because the object formats are not compatible.
+echo "
 CARGO_PROFILE_BENCH_INCREMENTAL=false
 CARGO_PROFILE_BENCH_LTO=false
 CARGO_PROFILE_RELEASE_INCREMENTAL=false
@@ -118,28 +120,27 @@ RUSTFLAGS<<__1
   -C linker-plugin-lto=true
   -C linker=clang-${llvmVersion}
   -C link-arg=-fuse-ld=lld-${llvmVersion}
-  -C link-arg=--sysroot=/sysroot
   -C link-arg=-ldl
   -C link-arg=-Wl,--allow-shlib-undefined
   -C link-arg=-Wl,--thinlto-cache-dir=$(pwd)/target/release/lto-cache
   -C link-arg=-Wl,--thinlto-cache-policy,cache_size_bytes=700m
   --cfg tokio_unstable
-  \${{ env.RUSTFLAGS }}
+  $RUSTFLAGS
 __1
 RUSTDOCFLAGS<<__1
   -C linker-plugin-lto=true
   -C linker=clang-${llvmVersion}
   -C link-arg=-fuse-ld=lld-${llvmVersion}
-  -C link-arg=--sysroot=/sysroot
   -C link-arg=-ldl
   -C link-arg=-Wl,--allow-shlib-undefined
   -C link-arg=-Wl,--thinlto-cache-dir=$(pwd)/target/release/lto-cache
   -C link-arg=-Wl,--thinlto-cache-policy,cache_size_bytes=700m
-  \${{ env.RUSTFLAGS }}
+  --cfg tokio_unstable
+  $RUSTFLAGS
 __1
 CC=/usr/bin/clang-${llvmVersion}
-CFLAGS=-flto=thin --sysroot=/sysroot
-__0`,
+CFLAGS=-flto=thin $CFLAGS
+" > $GITHUB_ENV`,
 };
 
 const installBenchTools = "./tools/install_prebuilt.js wrk hyperfine";
@@ -700,6 +701,24 @@ const ci = {
             "df -h",
           ].join("\n"),
         },
+        {
+          // Run a minimal check to ensure that binary is not corrupted, regardless
+          // of our build mode
+          name: "Check deno binary",
+          if: "matrix.job == 'test'",
+          run:
+            'target/${{ matrix.profile }}/deno eval "console.log(1+2)" | grep 3',
+          env: {
+            NO_COLOR: 1,
+          },
+        },
+        {
+          // Verify that the binary actually works in the Ubuntu-16.04 sysroot.
+          name: "Check deno binary (in sysroot)",
+          if: "matrix.job == 'test' && matrix.use_sysroot",
+          run:
+            'sudo chroot /sysroot "$(pwd)/target/${{ matrix.profile }}/deno" --version',
+        },
         {
           name: "Upload PR artifact (linux)",
           if: [
@@ -835,25 +854,6 @@ const ci = {
           ].join("\n"),
           run: "cargo test --release --locked",
         },
-        {
-          // Since all tests are skipped when we're building a tagged commit
-          // this is a minimal check to ensure that binary is not corrupted
-          name: "Check deno binary",
-          if:
-            "matrix.profile == 'release' && startsWith(github.ref, 'refs/tags/')",
-          run: 'target/release/deno eval "console.log(1+2)" | grep 3',
-          env: {
-            NO_COLOR: 1,
-          },
-        },
-        {
-          // Verify that the binary actually works in the Ubuntu-16.04 sysroot.
-          // TODO(mmastrac): make this work for aarch64 as well
-          name: "Check deno binary (in sysroot)",
-          if:
-            "matrix.profile == 'release' && matrix.use_sysroot && matrix.arch != 'aarch64'",
-          run: 'sudo chroot /sysroot "$(pwd)/target/release/deno" --version',
-        },
         {
           name: "Configure hosts file for WPT",
           if: "matrix.wpt",
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b7e463f11a..2f0207b101 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -273,7 +273,7 @@ jobs:
           (yes '' | sudo update-alternatives --force --all) > /dev/null 2> /dev/null || true
 
           echo "Decompressing sysroot..."
-          wget -q https://github.com/denoland/deno_sysroot_build/releases/download/sysroot-20240207/sysroot-`uname -m`.tar.xz -O /tmp/sysroot.tar.xz
+          wget -q https://github.com/denoland/deno_sysroot_build/releases/download/sysroot-20240527/sysroot-`uname -m`.tar.xz -O /tmp/sysroot.tar.xz
           cd /
           xzcat /tmp/sysroot.tar.xz | sudo tar -x
           sudo mount --rbind /dev /sysroot/dev
@@ -282,21 +282,23 @@ jobs:
           sudo mount -t proc /proc /sysroot/proc
           cd
 
-          if [[ `uname -m` == "aarch64" ]]; then
-            echo "Copying libdl.a"
-            sudo cp /sysroot/usr/lib/aarch64-linux-gnu/libdl.a /sysroot/lib/aarch64-linux-gnu/libdl.a
-            echo "Copying libdl.so"
-            sudo cp /sysroot/lib/aarch64-linux-gnu/libdl.so.2 /sysroot/lib/aarch64-linux-gnu/libdl.so
-          else
-            echo "Copying libdl.a"
-            sudo cp /sysroot/usr/lib/x86_64-linux-gnu/libdl.a /sysroot/lib/x86_64-linux-gnu/libdl.a
-            echo "Copying libdl.so"
-            sudo cp /sysroot/lib/x86_64-linux-gnu/libdl.so.2 /sysroot/lib/x86_64-linux-gnu/libdl.so
-          fi
+          echo "Done."
 
           # Configure the build environment. Both Rust and Clang will produce
           # llvm bitcode only, so we can use lld's incremental LTO support.
-          cat >> $GITHUB_ENV << __0
+
+          # Load the sysroot's env vars
+          echo "sysroot env:"
+          cat /sysroot/.env
+          . /sysroot/.env
+
+          # Important notes:
+          #   1. -ldl seems to be required to avoid a failure in FFI tests. This flag seems
+          #      to be in the Rust default flags in the smoketest, so uncertain why we need
+          #      to be explicit here.
+          #   2. RUSTFLAGS and RUSTDOCFLAGS must be specified, otherwise the doctests fail
+          #      to build because the object formats are not compatible.
+          echo "
           CARGO_PROFILE_BENCH_INCREMENTAL=false
           CARGO_PROFILE_BENCH_LTO=false
           CARGO_PROFILE_RELEASE_INCREMENTAL=false
@@ -305,28 +307,27 @@ jobs:
             -C linker-plugin-lto=true
             -C linker=clang-17
             -C link-arg=-fuse-ld=lld-17
-            -C link-arg=--sysroot=/sysroot
             -C link-arg=-ldl
             -C link-arg=-Wl,--allow-shlib-undefined
             -C link-arg=-Wl,--thinlto-cache-dir=$(pwd)/target/release/lto-cache
             -C link-arg=-Wl,--thinlto-cache-policy,cache_size_bytes=700m
             --cfg tokio_unstable
-            ${{ env.RUSTFLAGS }}
+            $RUSTFLAGS
           __1
           RUSTDOCFLAGS<<__1
             -C linker-plugin-lto=true
             -C linker=clang-17
             -C link-arg=-fuse-ld=lld-17
-            -C link-arg=--sysroot=/sysroot
             -C link-arg=-ldl
             -C link-arg=-Wl,--allow-shlib-undefined
             -C link-arg=-Wl,--thinlto-cache-dir=$(pwd)/target/release/lto-cache
             -C link-arg=-Wl,--thinlto-cache-policy,cache_size_bytes=700m
-            ${{ env.RUSTFLAGS }}
+            --cfg tokio_unstable
+            $RUSTFLAGS
           __1
           CC=/usr/bin/clang-17
-          CFLAGS=-flto=thin --sysroot=/sysroot
-          __0
+          CFLAGS=-flto=thin $CFLAGS
+          " > $GITHUB_ENV
       - name: Remove macOS cURL --ipv4 flag
         run: |-
           curl --version
@@ -419,6 +420,14 @@ jobs:
           df -h
           cargo build --release --locked --all-targets
           df -h
+      - name: Check deno binary
+        if: '!(matrix.skip) && (matrix.job == ''test'')'
+        run: 'target/${{ matrix.profile }}/deno eval "console.log(1+2)" | grep 3'
+        env:
+          NO_COLOR: 1
+      - name: Check deno binary (in sysroot)
+        if: '!(matrix.skip) && (matrix.job == ''test'' && matrix.use_sysroot)'
+        run: 'sudo chroot /sysroot "$(pwd)/target/${{ matrix.profile }}/deno" --version'
       - name: Upload PR artifact (linux)
         if: |-
           !(matrix.skip) && (matrix.job == 'test' &&
@@ -512,14 +521,6 @@ jobs:
           github.repository == 'denoland/deno' &&
           !startsWith(github.ref, 'refs/tags/'))))
         run: cargo test --release --locked
-      - name: Check deno binary
-        if: '!(matrix.skip) && (matrix.profile == ''release'' && startsWith(github.ref, ''refs/tags/''))'
-        run: target/release/deno eval "console.log(1+2)" | grep 3
-        env:
-          NO_COLOR: 1
-      - name: Check deno binary (in sysroot)
-        if: '!(matrix.skip) && (matrix.profile == ''release'' && matrix.use_sysroot && matrix.arch != ''aarch64'')'
-        run: sudo chroot /sysroot "$(pwd)/target/release/deno" --version
       - name: Configure hosts file for WPT
         if: '!(matrix.skip) && (matrix.wpt)'
         run: ./wpt make-hosts-file | sudo tee -a /etc/hosts