diff --git a/bin/fetch-cache-version b/bin/fetch-cache-version
new file mode 100755
index 00000000..572956f1
--- /dev/null
+++ b/bin/fetch-cache-version
@@ -0,0 +1,16 @@
+#!/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 -c '
+        split("\t")
+        | { "nextclade_version": .[0], "nextclade_dataset_version": .[1] }') \
+     2> /dev/null
diff --git a/bin/use-nextclade-cache b/bin/use-nextclade-cache
index 0a783dd1..f353f053 100755
--- a/bin/use-nextclade-cache
+++ b/bin/use-nextclade-cache
@@ -1,19 +1,40 @@
 #!/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="${3:?A path to the Nextclade executable is required as the third argument}"
+    nextclade_dataset="${4:?A path to a Nextclade dataset ZIP archive is required as the fourth argument}"
     # Nextclade dataset reference wildcard
-    reference="${3:-}"
+    reference="${5:-}"
+
     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 (${cache_nextclade_version})" >&2
+        echo "false"
+        exit 0
+    fi
+
+    cache_dataset_version="$(echo "$cache_versions" | jq -r .nextclade_dataset_version)"
+    current_dataset_version="$(unzip -p ${nextclade_dataset} pathogen.json | jq -r '.version.tag')"
+    if [[ "$cache_dataset_version" != "$current_dataset_version" ]]; then
+        echo "[INFO] Current Nextclade dataset version (${current_dataset_version}) is different from cache version (${cache_dataset_version})" >&2
+        echo "false"
+        exit 0
+    fi
+
     echo "true"
 }
 
@@ -25,4 +46,14 @@ 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}/${version_file}"
+    local src_version_file="${s3_src}/${version_file}"
+
+    "$bin"/fetch-cache-version "$dst_version_file" || "$bin"/cache-version "$src_version_file"
+}
+
 main "$@"
diff --git a/workflow/snakemake_rules/nextclade.smk b/workflow/snakemake_rules/nextclade.smk
index db56ecbf..9a2ff6cc 100644
--- a/workflow/snakemake_rules/nextclade.smk
+++ b/workflow/snakemake_rules/nextclade.smk
@@ -62,7 +62,22 @@ if config.get("s3_dst") and config.get("s3_src"):
     ruleorder: download_nextclade_tsv_from_s3 > create_empty_nextclade_info
     ruleorder: download_previous_alignment_from_s3 > create_empty_nextclade_aligned
 
+    def _convert_dataset_name(wildcards):
+        if wildcards.reference == '':
+            dataset_name="sars-cov-2"
+        elif wildcards.reference == '_21L':
+            dataset_name="sars-cov-2-21L"
+        else:
+            # We shouldn't run into this since we have wildcard_constraints,
+            # but doesn't hurt to include it in case that changes
+            raise ValueError(f"Cannot convert unsupported reference {wildcards.reference!r} to Nextclade dataset name")
+
+        return f"data/nextclade_data/{dataset_name}.zip",
+
     rule use_nextclade_cache:
+        input:
+            nextclade="./nextclade",
+            nextclade_dataset=_convert_dataset_name,
         params:
             dst_source=config["s3_dst"],
             src_source=config["s3_src"],
@@ -73,6 +88,8 @@ 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} \
+                {input.nextclade_dataset:q} \
                 {wildcards.reference:q} \
                 > {output.use_nextclade_cache}
             """