diff --git a/aviary/aviary.py b/aviary/aviary.py
index aad581d..95beaf3 100755
--- a/aviary/aviary.py
+++ b/aviary/aviary.py
@@ -153,6 +153,13 @@ def main():
         default=8,
     )
 
+    base_group.add_argument(
+        '-p', '--pplacer-threads', '--pplacer_threads',
+        help='The number of threads given to pplacer, values above 48 will be scaled down',
+        dest='pplacer_threads',
+        default=48,
+    )
+
     base_group.add_argument(
         '-n', '--n-cores', '--n_cores',
         help='Maximum number of cores available for use. Setting to multiples of max_threads will allow for multiple processes to be run in parallel.',
diff --git a/aviary/modules/processor.py b/aviary/modules/processor.py
index 2f247bf..b6a1a18 100644
--- a/aviary/modules/processor.py
+++ b/aviary/modules/processor.py
@@ -99,10 +99,14 @@ def __init__(self,
         self.output = os.path.abspath(args.output)
         self.threads = args.max_threads
         self.max_memory = args.max_memory
-        self.pplacer_threads = min(int(self.threads), 48)
         self.workflows = args.workflow
         self.request_gpu = args.request_gpu
 
+        try:
+            self.pplacer_threads = min(int(args.pplacer_threads), int(self.threads), 48)
+        except AttributeError:
+            self.pplacer_threads = min(int(self.threads), 48)
+
         try:
             self.strain_analysis = args.strain_analysis
         except AttributeError:
diff --git a/test/test_recover.py b/test/test_recover.py
index d1775d0..5bd2aad 100644
--- a/test/test_recover.py
+++ b/test/test_recover.py
@@ -358,6 +358,7 @@ def test_recover_config(self):
                 f"SINGLEM_METAPACKAGE_PATH=. "
                 f"aviary recover "
                 f"--refinery-max-iterations 3 "
+                f"--max-threads 8 "
                 f"--assembly {ASSEMBLY} "
                 f"-1 {FORWARD_READS} "
                 f"-2 {REVERSE_READS} "
@@ -373,6 +374,60 @@ def test_recover_config(self):
             config = load_configfile(config_path)
 
             self.assertEqual(config["refinery_max_iterations"], 3)
+            self.assertEqual(config["pplacer_threads"], 8)
+
+    def test_recover_config_many_threads(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            cmd = (
+                f"GTDBTK_DATA_PATH=. "
+                f"CHECKM2DB=. "
+                f"EGGNOG_DATA_DIR=. "
+                f"SINGLEM_METAPACKAGE_PATH=. "
+                f"aviary recover "
+                f"--max-threads 128 "
+                f"--assembly {ASSEMBLY} "
+                f"-1 {FORWARD_READS} "
+                f"-2 {REVERSE_READS} "
+                f"--output {tmpdir}/test --tmpdir {tmpdir} "
+                f"--conda-prefix {path_to_conda} "
+                f"--dryrun "
+                f"--snakemake-cmds \" --quiet\" "
+            )
+            extern.run(cmd)
+
+            config_path = os.path.join(tmpdir, "test", "config.yaml")
+            self.assertTrue(os.path.exists(config_path))
+            config = load_configfile(config_path)
+
+            self.assertEqual(config["refinery_max_iterations"], 5)
+            self.assertEqual(config["pplacer_threads"], 48)
+
+    def test_recover_config_many_pplacer_threads(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            cmd = (
+                f"GTDBTK_DATA_PATH=. "
+                f"CHECKM2DB=. "
+                f"EGGNOG_DATA_DIR=. "
+                f"SINGLEM_METAPACKAGE_PATH=. "
+                f"aviary recover "
+                f"--max-threads 128 "
+                f"--pplacer-threads 32 "
+                f"--assembly {ASSEMBLY} "
+                f"-1 {FORWARD_READS} "
+                f"-2 {REVERSE_READS} "
+                f"--output {tmpdir}/test --tmpdir {tmpdir} "
+                f"--conda-prefix {path_to_conda} "
+                f"--dryrun "
+                f"--snakemake-cmds \" --quiet\" "
+            )
+            extern.run(cmd)
+
+            config_path = os.path.join(tmpdir, "test", "config.yaml")
+            self.assertTrue(os.path.exists(config_path))
+            config = load_configfile(config_path)
+
+            self.assertEqual(config["refinery_max_iterations"], 5)
+            self.assertEqual(config["pplacer_threads"], 32)
 
 if __name__ == '__main__':
     unittest.main()