diff --git a/augur/ancestral.py b/augur/ancestral.py
index 64b25d6fe..fde4b5bbe 100644
--- a/augur/ancestral.py
+++ b/augur/ancestral.py
@@ -228,15 +228,32 @@ def register_parser(parent_subparsers):
 
     return parser
 
-def run(args):
-    # Validate arguments.
+def check_arg_combinations(args, is_vcf):
+    """
+    Check that provided arguments are compatible.
+    Where possible we use argparse built-ins, but they don't cover everything we want to check.
+    This checking shouldn't be used by downstream code to assume arguments exist, however by checking for
+    invalid combinations up-front we can exit quickly.
+    """
     aa_arguments = (args.annotation, args.genes, args.translations)
     if any(aa_arguments) and not all(aa_arguments):
         raise AugurError("For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences.")
 
+    if args.output_sequences and args.output_vcf:
+        raise AugurError("Both sequence (fasta) and VCF output have been requested, but these are incompatible.")
+    
+    if is_vcf and args.output_sequences:
+        raise AugurError("Sequence (fasta) output has been requested but the input alignment is VCF.")
+
+    if not is_vcf and args.output_vcf:
+        raise AugurError("VCF output has been requested but the input alignment is not VCF.")
+
+
+def run(args):
     # check alignment type, set flags, read in if VCF
     is_vcf = any([args.alignment.lower().endswith(x) for x in ['.vcf', '.vcf.gz']])
     ref = None
+    check_arg_combinations(args, is_vcf)
 
     try:
         T = read_tree(args.tree)
@@ -351,19 +368,13 @@ def run(args):
     write_json(anc_seqs, out_name)
     print("ancestral mutations written to", out_name, file=sys.stdout)
 
-    if args.output_sequences:
-        if args.output_vcf:
-            # TODO: This should be an error and we should check for this
-            # unsupported combination of arguments at the beginning of the
-            # script to avoid wasting time for users.
-            print("WARNING: augur only supports sequence output for FASTA alignments and not for VCFs.", file=sys.stderr)
-        else:
-            records = [
-                SeqRecord(Seq(node_data["sequence"]), id=node_name, description="")
-                for node_name, node_data in anc_seqs["nodes"].items()
-            ]
-            SeqIO.write(records, args.output_sequences, "fasta")
-            print("ancestral sequences FASTA written to", args.output_sequences, file=sys.stdout)
+    if not is_vcf and args.output_sequences:
+        records = [
+            SeqRecord(Seq(node_data["sequence"]), id=node_name, description="")
+            for node_name, node_data in anc_seqs["nodes"].items()
+        ]
+        SeqIO.write(records, args.output_sequences, "fasta")
+        print("ancestral sequences FASTA written to", args.output_sequences, file=sys.stdout)
 
     # If VCF, output VCF including new ancestral seqs
     if is_vcf:
diff --git a/tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t b/tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t
deleted file mode 100644
index 3fd014296..000000000
--- a/tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t
+++ /dev/null
@@ -1,15 +0,0 @@
-Setup
-
-  $ source "$TESTDIR"/_setup.sh
-
-Try to infer ancestral amino acid sequences without all required arguments.
-This should fail.
-
-  $ ${AUGUR} ancestral \
-  >  --tree $TESTDIR/../data/tree.nwk \
-  >  --alignment $TESTDIR/../data/aligned.fasta \
-  >  --annotation $TESTDIR/../data/zika_outgroup.gb \
-  >  --genes ENV PRO \
-  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null
-  ERROR: For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences.
-  [2]
diff --git a/tests/functional/ancestral/cram/invalid-args.t b/tests/functional/ancestral/cram/invalid-args.t
new file mode 100644
index 000000000..40075dc58
--- /dev/null
+++ b/tests/functional/ancestral/cram/invalid-args.t
@@ -0,0 +1,44 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Input FASTA + VCF output is not possible
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --output-vcf "$CRAMTMP/$TESTFILE/output.vcf" > /dev/null
+  ERROR: VCF output has been requested but the input alignment is not VCF.
+  [2]
+
+Input VCF + FASTA output is not possible (Note that the input file doesn't exist, but we exit before that's checked)
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/snps.vcf \
+  >  --output-sequences "$CRAMTMP/$TESTFILE/output.fasta" > /dev/null
+  ERROR: Sequence (fasta) output has been requested but the input alignment is VCF.
+  [2]
+
+Output FASTA _and_ VCF is not possible
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --output-vcf "$CRAMTMP/$TESTFILE/output.vcf" \
+  >  --output-sequences "$CRAMTMP/$TESTFILE/output.fasta" > /dev/null
+  ERROR: Both sequence (fasta) and VCF output have been requested, but these are incompatible.
+  [2]
+
+
+Try to infer ancestral amino acid sequences without all required arguments.
+This should fail.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --annotation $TESTDIR/../data/zika_outgroup.gb \
+  >  --genes ENV PRO \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null
+  ERROR: For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences.
+  [2]