diff --git a/src/fastgather.rs b/src/fastgather.rs
index 46512025..08a1ebbd 100644
--- a/src/fastgather.rs
+++ b/src/fastgather.rs
@@ -1,4 +1,5 @@
 /// fastgather: Run gather with a query against a list of files.
+use pyo3::Python;
 use anyhow::Result;
 use sourmash::prelude::Select;
 use sourmash::selection::Selection;
@@ -10,6 +11,7 @@ use crate::utils::{
 
 #[allow(clippy::too_many_arguments)]
 pub fn fastgather(
+    py: Python,
     query_filepath: String,
     against_filepath: String,
     threshold_bp: usize,
@@ -94,6 +96,7 @@ pub fn fastgather(
 
     // run the gather!
     consume_query_by_gather(
+        py,
         query_sig,
         scaled as u64,
         matchlist,
diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs
index 608fc215..e58b6aac 100644
--- a/src/fastmultigather.rs
+++ b/src/fastmultigather.rs
@@ -1,6 +1,7 @@
 /// fastmultigather: Run gather for multiple queries against a list of files.
 use anyhow::Result;
 use rayon::prelude::*;
+use pyo3::Python;
 
 use sourmash::selection::Selection;
 
@@ -17,6 +18,7 @@ use crate::utils::{
 };
 
 pub fn fastmultigather(
+    py: Python,
     query_filepath: String,
     against_filepath: String,
     threshold_bp: usize,
@@ -98,6 +100,7 @@ pub fn fastmultigather(
 
                         // Now, do the gather!
                         consume_query_by_gather(
+                            py,
                             query_sig.clone(),
                             scaled as u64,
                             matchlist,
diff --git a/src/lib.rs b/src/lib.rs
index e8d22f2a..4567e03f 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -23,6 +23,7 @@ use camino::Utf8PathBuf as PathBuf;
 
 #[pyfunction]
 fn do_manysearch(
+    py: Python,
     querylist_path: String,
     siglist_path: String,
     threshold: f64,
@@ -73,6 +74,7 @@ fn do_manysearch(
 #[pyfunction]
 #[allow(clippy::too_many_arguments)]
 fn do_fastgather(
+    py: Python,
     query_filename: String,
     siglist_path: String,
     threshold_bp: usize,
@@ -86,6 +88,7 @@ fn do_fastgather(
     let allow_failed_sigpaths = true;
 
     match fastgather::fastgather(
+        py,
         query_filename,
         siglist_path,
         threshold_bp,
@@ -105,6 +108,7 @@ fn do_fastgather(
 
 #[pyfunction]
 fn do_fastmultigather(
+    py: Python,
     query_filenames: String,
     siglist_path: String,
     threshold_bp: usize,
@@ -138,6 +142,7 @@ fn do_fastmultigather(
             bail!("output path specified, but not running fastmultigather against a rocksdb. See issue #239");
         }
         match fastmultigather::fastmultigather(
+            py,
             query_filenames,
             siglist_path,
             threshold_bp,
@@ -173,6 +178,7 @@ fn set_global_thread_pool(num_threads: usize) -> PyResult<usize> {
 
 #[pyfunction]
 fn do_index(
+    py: Python,
     siglist: String,
     ksize: u8,
     scaled: usize,
@@ -206,6 +212,7 @@ fn do_check(index: String, quick: bool) -> anyhow::Result<u8> {
 #[pyfunction]
 #[allow(clippy::too_many_arguments)]
 fn do_multisearch(
+    py: Python,
     querylist_path: String,
     siglist_path: String,
     threshold: f64,
@@ -238,6 +245,7 @@ fn do_multisearch(
 #[pyfunction]
 #[allow(clippy::too_many_arguments)]
 fn do_pairwise(
+    py: Python,
     siglist_path: String,
     threshold: f64,
     ksize: u8,
@@ -268,6 +276,7 @@ fn do_pairwise(
 
 #[pyfunction]
 fn do_manysketch(
+    py: Python,
     filelist: String,
     param_str: String,
     output: String,
@@ -285,6 +294,7 @@ fn do_manysketch(
 
 #[pyfunction]
 fn do_cluster(
+    py: Python,
     pairwise_csv: String,
     output_clusters: String,
     similarity_column: String,
diff --git a/src/utils.rs b/src/utils.rs
index 89779133..ae123abb 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -1,5 +1,6 @@
 /// Utility functions for sourmash_plugin_branchwater.
 use rayon::prelude::*;
+use pyo3::Python;
 use sourmash::encodings::HashFunctions;
 use sourmash::selection::Select;
 
@@ -926,6 +927,7 @@ pub fn branchwater_calculate_gather_stats(
 /// removing matches in 'matchlist' from 'query'.
 
 pub fn consume_query_by_gather(
+    py: Python,
     query: SigStore,
     scaled: u64,
     matchlist: BinaryHeap<PrefetchResult>,
@@ -994,6 +996,7 @@ pub fn consume_query_by_gather(
     );
 
     while !matching_sketches.is_empty() {
+        py.check_signals()?;
         let best_element = matching_sketches.peek().unwrap();
 
         query_mh = query_mh.downsample_scaled(best_element.minhash.scaled())?;