diff --git a/bin/cache-version b/bin/cache-version
new file mode 100644
index 00000000..13940869
--- /dev/null
+++ b/bin/cache-version
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+s3_url="${1:?An S3 URL is required as the first argument}"
+
+
+trap '' SIGPIPE
+
+(aws s3 cp "${s3_url}" - \
+    | zstd -T0 -dcq \
+    | head -n 2 \
+    | tsv-select -H -f 'nextclade_version,dataset_version' \
+    | tail -n 1 \
+    | jq --raw-input --slurp '
+        split("\n")
+        | map(split("\t"))
+        | .[0:-1]
+        | map( { "nextclade_version": .[0], "nextclade_dataset_version": .[1] } )
+        | .[0]') \
+     2> /dev/null
diff --git a/bin/use-nextclade-cache b/bin/use-nextclade-cache
index 0a783dd1..8dadb9a9 100755
--- a/bin/use-nextclade-cache
+++ b/bin/use-nextclade-cache
@@ -1,19 +1,31 @@
 #!/bin/bash
 set -euo pipefail
 
-vendored="$(dirname "$0")"/../vendored
+bin="$(dirname "$0")"
+vendored="$bin"/../vendored
 
 main() {
     s3_dst="${1:?A destination s3:// URL where the renew file is hosted is required as the first argument.}"
     s3_src="${2:?A source s3:// URL where the fallback renew file is hosted is required as the second argument.}"
+    nextclade="${3:?A path to the Nextclade executable is required as the third argument}"
     # Nextclade dataset reference wildcard
-    reference="${3:-}"
+    reference="${4:-}"
+
     if renew-flag-exists; then
         echo "[INFO] Found renew flag" >&2
         echo "false"
         exit 0
     fi
 
+    cache_versions="$(get-cache-version-info)"
+    cache_nextclade_version="$(echo "$cache_versions" | jq -r .nextclade_version)"
+    current_nextclade_version="$("$nextclade" --version)"
+    if [[ "$cache_nextclade_version" != "$current_nextclade_version" ]]; then
+        echo "[INFO] Current Nextclade version (${current_nextclade_version}) is different from cache version (${cache_nextclade_version})" >&2
+        echo "false"
+        exit 0
+    fi
+
     echo "true"
 }
 
@@ -25,4 +37,13 @@ renew-flag-exists() {
     "$vendored"/s3-object-exists "${dst_renew_file}" || "$vendored"/s3-object-exists "${src_renew_file}"
 }
 
+get-cache-version-info() {
+    # TODO: Update check a separate file for version info
+    # Currently just checks the first row of the nextclade.tsv file
+    local version_file="nextclade${reference}.tsv.zst"
+    local dst_version_file="${s3_dst}/${version_file}"
+
+    echo "$("$bin"/cache-version "$dst_version_file")"
+}
+
 main "$@"
diff --git a/workflow/snakemake_rules/nextclade.smk b/workflow/snakemake_rules/nextclade.smk
index db56ecbf..3c366034 100644
--- a/workflow/snakemake_rules/nextclade.smk
+++ b/workflow/snakemake_rules/nextclade.smk
@@ -63,6 +63,8 @@ if config.get("s3_dst") and config.get("s3_src"):
     ruleorder: download_previous_alignment_from_s3 > create_empty_nextclade_aligned
 
     rule use_nextclade_cache:
+        input:
+            nextclade="nextclade",
         params:
             dst_source=config["s3_dst"],
             src_source=config["s3_src"],
@@ -73,6 +75,7 @@ if config.get("s3_dst") and config.get("s3_src"):
             ./bin/use-nextclade-cache \
                 {params.dst_source:q} \
                 {params.src_source:q} \
+                {input.nextclade:q} \
                 {wildcards.reference:q} \
                 > {output.use_nextclade_cache}
             """