diff --git a/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml b/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
index af6ec9da2cf0..4dc9dfc63ef7 100644
--- a/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar diagram (jqPlot)">
+<visualization name="Bar diagram (jqPlot)" visible="false">
     <macros>
         <import>jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml b/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
index 93d559089053..0e440be10e82 100644
--- a/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Box plot (jqPlot)" embeddable="false">
+<visualization name="Box plot (jqPlot)" embeddable="false" visible="false">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml b/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
index e38ec98c0af5..7537a379893f 100644
--- a/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Discrete Histogram (jqPlot)" embeddable="false">
+<visualization name="Discrete Histogram (jqPlot)" embeddable="false" visible="false">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml b/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
index b2255cdf3e06..2791123bb260 100644
--- a/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Line chart (jqPlot)">
+<visualization name="Line chart (jqPlot)" visible="false">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml b/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
index e88a693311e6..7347b2717d34 100644
--- a/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Scatter plot (jqPlot)">
+<visualization name="Scatter plot (jqPlot)" visible="false">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
index ebc6e765d08a..94e55dd22e6d 100644
--- a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar diagram (NVD3)">
+<visualization name="Bar diagram (NVD3)" visible="false">
     <macros>
         <import>nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml b/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
index 6fb0a3f2b401..81e6c652f2d2 100644
--- a/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar Stacked (NVD3)">
+<visualization name="Bar Stacked (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml b/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
index 159bd6bd90bb..7db9332b905e 100644
--- a/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Histogram (NVD3)" embeddable="false">
+<visualization name="Histogram (NVD3)" embeddable="false" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml b/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
index a32f52001ee8..3dcfc0a03575 100644
--- a/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Histogram Discrete (NVD3)" embeddable="false">
+<visualization name="Histogram Discrete (NVD3)" embeddable="false" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml b/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
index 15e2050f2183..39b66e5f7024 100644
--- a/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar Horizontal (NVD3)">
+<visualization name="Bar Horizontal (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml b/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
index f5710f72dd89..4875c8dcb913 100644
--- a/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar Horizontal Stacked (NVD3)">
+<visualization name="Bar Horizontal Stacked (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml b/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
index bcdd01e1f817..0a0145a2e74b 100644
--- a/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Line chart (NVD3)">
+<visualization name="Line chart (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml b/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
index f6dac98cbf82..8998dc8aeeaa 100644
--- a/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Line with focus (NVD3)">
+<visualization name="Line with focus (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml b/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
index 093543e25593..3e28b302506c 100644
--- a/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Pie chart (NVD3)">
+<visualization name="Pie chart (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml b/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
index 05399c0c81d5..148e07569778 100644
--- a/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Scatter plot (NVD3)">
+<visualization name="Scatter plot (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml b/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
index ef2e4ae1b19d..ab21737e50c4 100644
--- a/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Stacked area (NVD3)">
+<visualization name="Stacked area (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml b/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
index bfc4dc2e63f4..c25cf714e43f 100644
--- a/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Expanded (NVD3)">
+<visualization name="Expanded (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml b/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
index f11aa05aa36f..a34df97a071a 100644
--- a/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Stream (NVD3)">
+<visualization name="Stream (NVD3)" visible="false">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/scatterplot/config/scatterplot.xml b/config/plugins/visualizations/scatterplot/config/scatterplot.xml
index 9f3121e2bebd..606aa04864e8 100644
--- a/config/plugins/visualizations/scatterplot/config/scatterplot.xml
+++ b/config/plugins/visualizations/scatterplot/config/scatterplot.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Scatterplot">
+<visualization name="Scatterplot" visible="false">
     <description>Creates a 2D-scatterplot from tabular datapoints</description>
     <data_sources>
         <data_source>
diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index ffefbe2dfb8a..a26c6fd20845 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -80,6 +80,11 @@ def parse_visualization(self, xml_tree):
         if "embeddable" in xml_tree.attrib:
             returned["embeddable"] = asbool(xml_tree.attrib.get("embeddable"))
 
+        # record the visible flag - defaults to true
+        returned["visible"] = True
+        if "visible" in xml_tree.attrib:
+            returned["visible"] = asbool(xml_tree.attrib.get("visible"))
+
         # a (for now) text description of what the visualization does
         description = xml_tree.find("description")
         returned["description"] = description.text.strip() if description is not None else None
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
index bd293dca85b0..8d7141b3067b 100644
--- a/lib/galaxy/visualization/plugins/registry.py
+++ b/lib/galaxy/visualization/plugins/registry.py
@@ -225,26 +225,22 @@ def get_plugin(self, key):
             raise ObjectNotFound(f"Unknown or invalid visualization: {key}")
         return self.plugins[key]
 
-    def get_plugins(self, embeddable=None):
-        result = []
-        for plugin in self.plugins.values():
-            if embeddable and not plugin.config.get("embeddable"):
-                continue
-            result.append(plugin.to_dict())
-        return sorted(result, key=lambda k: k.get("html"))
-
     # -- building links to visualizations from objects --
-    def get_visualizations(self, trans, target_object):
+    def get_visualizations(self, trans, target_object=None, embeddable=None):
         """
         Get the names of visualizations usable on the `target_object` and
         the urls to call in order to render the visualizations.
         """
-        applicable_visualizations = []
-        for vis_name in self.plugins:
-            url_data = self.get_visualization(trans, vis_name, target_object)
-            if url_data:
-                applicable_visualizations.append(url_data)
-        return sorted(applicable_visualizations, key=lambda k: k.get("html"))
+        result = []
+        for vis_name, vis_plugin in self.plugins.items():
+            if not vis_plugin.config.get("visible"):
+                continue
+            if embeddable and not vis_plugin.config.get("embeddable"):
+                continue
+            if target_object is not None and self.get_visualization(trans, vis_name, target_object) is None:
+                continue
+            result.append(vis_plugin.to_dict())
+        return sorted(result, key=lambda k: k.get("html"))
 
     def get_visualization(self, trans, visualization_name, target_object):
         """
diff --git a/lib/galaxy/webapps/galaxy/api/plugins.py b/lib/galaxy/webapps/galaxy/api/plugins.py
index d8af00154ea1..d1f861b57cf2 100644
--- a/lib/galaxy/webapps/galaxy/api/plugins.py
+++ b/lib/galaxy/webapps/galaxy/api/plugins.py
@@ -36,12 +36,11 @@ def index(self, trans, **kwargs):
         GET /api/plugins:
         """
         registry = self._get_registry()
+        embeddable = asbool(kwargs.get("embeddable"))
+        target_object = None
         if (dataset_id := kwargs.get("dataset_id")) is not None:
-            hda = self.hda_manager.get_accessible(self.decode_id(dataset_id), trans.user)
-            return registry.get_visualizations(trans, hda)
-        else:
-            embeddable = asbool(kwargs.get("embeddable"))
-            return registry.get_plugins(embeddable=embeddable)
+            target_object = self.hda_manager.get_accessible(self.decode_id(dataset_id), trans.user)
+        return registry.get_visualizations(trans, target_object=target_object, embeddable=embeddable)
 
     @expose_api
     def show(self, trans, id, **kwargs):