diff --git a/scripts/ci/assemble_e2e_benchmark.sh b/scripts/ci/assemble_e2e_benchmark.sh
index 647e3cbcd97..90291ffa8b8 100755
--- a/scripts/ci/assemble_e2e_benchmark.sh
+++ b/scripts/ci/assemble_e2e_benchmark.sh
@@ -4,38 +4,37 @@
 # and assembles a single file that shows the current state of the repository.
 
 [ -n "${BUILD_SYSTEM_DEBUG:-}" ] && set -x # conditionally trace
-
-# Enter yarn-project dir.
-cd "$(dirname $0)/../../yarn-project/"
 set -eu
 
-PULL_REQUEST_ID=$1
-BRANCH=$2
 BUCKET_NAME="aztec-ci-artifacts"
-COMMIT_HASH=$3
+LOG_FOLDER="${LOG_FOLDER:-log}"
+BENCH_FOLDER="${BENCH_FOLDER:-bench}"
+COMMIT_HASH="${COMMIT_HASH:-$(git rev-parse HEAD)}"
 BASE_BENCH_PATH=""
+BENCHMARK_FILE_JSON="${BENCH_FOLDER}/benchmark.json"
+BASE_BENCHMARK_FILE_JSON="${BENCH_FOLDER}/base-benchmark.json"
 
-# Paths from scripts/upload_logs_to_s3
-if [ "${BRANCH:-}" = "master" ]; then
+# Paths from build-system/scripts/upload_logs_to_s3
+if [ "${CIRCLE_BRANCH:-}" = "master" ]; then
   LOG_SOURCE_FOLDER="logs-v1/master/$COMMIT_HASH"
   BARRETENBERG_BENCH_SOURCE_FOLDER="barretenberg-bench-v1/master/$COMMIT_HASH"
   BENCHMARK_TARGET_FILE="benchmarks-v1/master/$COMMIT_HASH.json"
   BENCHMARK_LATEST_FILE="benchmarks-v1/latest.json"
-elif [ -n "$PULL_REQUEST_ID" ]; then
-  LOG_SOURCE_FOLDER="logs-v1/pulls/${PULL_REQUEST_ID##*/}"
-  BARRETENBERG_BENCH_SOURCE_FOLDER="barretenberg-bench-v1/pulls/${PULL_REQUEST_ID##*/}"
-  BENCHMARK_TARGET_FILE="benchmarks-v1/pulls/${PULL_REQUEST_ID##*/}.json"
+elif [ -n "${CIRCLE_PULL_REQUEST:-}" ]; then
+  LOG_SOURCE_FOLDER="logs-v1/pulls/${CIRCLE_PULL_REQUEST##*/}"
+  BARRETENBERG_BENCH_SOURCE_FOLDER="barretenberg-bench-v1/pulls/${CIRCLE_PULL_REQUEST##*/}"
+  BENCHMARK_TARGET_FILE="benchmarks-v1/pulls/${CIRCLE_PULL_REQUEST##*/}.json"
 elif [ -n "${CIRCLE_TAG:-}" ]; then
   echo "Skipping benchmark run for ${CIRCLE_TAG} tagged release."
   exit 0
 else
-  echo "Skipping benchmark run on branch ${BRANCH:-unknown}."
+  echo "Skipping benchmark run on branch ${CIRCLE_BRANCH:-unknown}."
   exit 0
 fi
 
-# Download benchmark log files from S3 LOG_SOURCE_FOLDER into local 'log' folder
-mkdir -p log
-aws s3 cp "s3://${BUCKET_NAME}/${LOG_SOURCE_FOLDER}/" log --exclude '*' --include 'bench*.jsonl' --recursive
+# Download benchmark log files from S3 LOG_SOURCE_FOLDER into local LOG_FOLDER
+mkdir -p $LOG_FOLDER
+aws s3 cp "s3://${BUCKET_NAME}/${LOG_SOURCE_FOLDER}/" $LOG_FOLDER --exclude '*' --include 'bench*.jsonl' --recursive
 
 # Only generate the aggregated benchmark if we've managed to retrieve all the needed log files
 # If these runs were skipped due to no changes in their rebuild-patterns, then there's no need
@@ -43,25 +42,60 @@ aws s3 cp "s3://${BUCKET_NAME}/${LOG_SOURCE_FOLDER}/" log --exclude '*' --includ
 # this skips the whole aggregation. For now, that's fine because all benchmark files have the
 # same rebuild pattern rules. But if that changes, then we'd need to go up in the commit history
 # to find the latest log files for the unchanged benchmarks.
-EXPECTED_LOGS_COUNT=$(find end-to-end/src -type f -name "bench*.test.ts" | wc -l)
-DOWNLOADED_LOGS_COUNT=$(find log -type f -name "*.jsonl" | wc -l)
+EXPECTED_LOGS_COUNT=$(find yarn-project/end-to-end/src -type f -name "bench*.test.ts" | wc -l)
+DOWNLOADED_LOGS_COUNT=$(find $LOG_FOLDER -type f -name "*.jsonl" | wc -l)
 if [ "$DOWNLOADED_LOGS_COUNT" -lt "$EXPECTED_LOGS_COUNT" ]; then
   echo Found $DOWNLOADED_LOGS_COUNT out of $EXPECTED_LOGS_COUNT benchmark log files in s3://${BUCKET_NAME}/${LOG_SOURCE_FOLDER}/. Exiting.
   exit 0
 fi
 
 # Download barretenberg log files, these are direct benchmarks and separate from the above
-aws s3 cp "s3://${BUCKET_NAME}/${BARRETENBERG_BENCH_SOURCE_FOLDER}/" log --exclude '*' --include '*_bench.json' --recursive
+aws s3 cp "s3://${BUCKET_NAME}/${BARRETENBERG_BENCH_SOURCE_FOLDER}/" $LOG_FOLDER --exclude '*' --include '*_bench.json' --recursive
 
 # Generate the aggregated benchmark file
-# TODO rename CIRCLE_PULL_REQUEST to PULL_REQUEST_ID
-CIRCLE_PULL_REQUEST=$PULL_REQUEST_ID LOG_FOLDER=$(pwd)/log yarn workspace @aztec/scripts bench-aggregate
-echo "generated: scripts/bench/benchmark.json"
+mkdir -p $BENCH_FOLDER
+CONTAINER_BENCH_FOLDER="/usr/src/yarn-project/bench"
+CONTAINER_LOG_FOLDER="/usr/src/yarn-project/log"
+export DOCKER_RUN_OPTS="\
+ -v $(realpath $BENCH_FOLDER):${CONTAINER_BENCH_FOLDER}:rw \
+ -e BENCH_FOLDER=${CONTAINER_BENCH_FOLDER} \
+ -v $(realpath $LOG_FOLDER):${CONTAINER_LOG_FOLDER}:rw \
+ -e LOG_FOLDER=${CONTAINER_LOG_FOLDER} \
+ -e BASE_BENCH_PATH \
+ -e AZTEC_BOT_COMMENTER_GITHUB_TOKEN \
+ -e CIRCLE_PULL_REQUEST"
+yarn-project/scripts/run_script.sh workspace @aztec/scripts bench-aggregate
+echo "generated: $BENCHMARK_FILE_JSON"
 
 # Upload it to master or pulls
-aws s3 cp scripts/bench/benchmark.json "s3://${BUCKET_NAME}/${BENCHMARK_TARGET_FILE}"
+aws s3 cp $BENCHMARK_FILE_JSON "s3://${BUCKET_NAME}/${BENCHMARK_TARGET_FILE}"
 
 # If on master, also update the "latest" benchmark file
 if [ -n "${BENCHMARK_LATEST_FILE:-}" ]; then
-  aws s3 cp scripts/bench/benchmark.json "s3://${BUCKET_NAME}/${BENCHMARK_LATEST_FILE}"
+  aws s3 cp $BENCHMARK_FILE_JSON "s3://${BUCKET_NAME}/${BENCHMARK_LATEST_FILE}"
+fi
+
+# If on a pull request, get the data from the most recent commit on master where it's available,
+# generate a markdown comment, and post it on the pull request
+if [ -n "${CIRCLE_PULL_REQUEST:-}" ]; then
+  MASTER_COMMIT_HASH=$(curl -s "https://api.github.com/repos/AztecProtocol/aztec-packages/pulls/${CIRCLE_PULL_REQUEST##*/}" | jq -r '.base.sha')
+  MASTER_COMMIT_HASHES=($(git log $MASTER_COMMIT_HASH --format="%H" -n 50))
+
+  set +e
+  echo "Searching for base benchmark data starting from commit $MASTER_COMMIT_HASH"
+  for commit_hash in "${MASTER_COMMIT_HASHES[@]}"; do
+    aws s3 cp "s3://${BUCKET_NAME}/benchmarks-v1/master/$commit_hash.json" $BASE_BENCHMARK_FILE_JSON
+    if [ $? -eq 0 ]; then
+      echo "Downloaded base data from commit $commit_hash"
+      export BASE_BENCH_PATH=master/$commit_hash
+      break;
+    fi
+  done
+  set -e
+
+  if [ -z "${BASE_BENCH_PATH:-}" ]; then
+    echo "No base commit data found"
+  fi
+
+  (yarn-project/scripts/run_script.sh workspace @aztec/scripts bench-comment && echo "commented on pr $CIRCLE_PULL_REQUEST") || echo "failed commenting on pr"
 fi