diff --git a/qiita_db/software.py b/qiita_db/software.py
index 171490597..a21f8c4d0 100644
--- a/qiita_db/software.py
+++ b/qiita_db/software.py
@@ -622,11 +622,26 @@ def active(self):
         -------
         bool
             Whether the command is active or not
+
+        Notes
+        -----
+        This method differentiates between commands based on analysis_only. The
+        commands that are not for analysis (processing) will return as active
+        if they have the same name than a command that is active; this helps
+        for situations where the processing plugins are updated but some
+        commands didn't change its version.
         """
         with qdb.sql_connection.TRN:
-            sql = """SELECT active
-                     FROM qiita.software_command
-                     WHERE command_id = %s"""
+            if self.analysis_only:
+                sql = """SELECT active
+                         FROM qiita.software_command
+                         WHERE command_id = %s"""
+            else:
+                sql = """SELECT EXISTS (
+                            SELECT active FROM qiita.software_command
+                            WHERE name IN (
+                                SELECT name FROM qiita.software_command
+                                WHERE command_id = %s) AND active = true)"""
             qdb.sql_connection.TRN.add(sql, [self.id])
             return qdb.sql_connection.TRN.execute_fetchlast()
 
diff --git a/qiita_db/test/test_software.py b/qiita_db/test/test_software.py
index 022fd0889..59cb468fe 100644
--- a/qiita_db/test/test_software.py
+++ b/qiita_db/test/test_software.py
@@ -334,6 +334,13 @@ def test_create_error(self):
                 self.outputs)
 
     def test_create(self):
+        # let's deactivate all current plugins and commands; this is not
+        # important to test the creation but it is important to test if a
+        # command is active as the new commands should take precedence and
+        # should make the old commands active if they have the same name
+        qdb.software.Software.deactivate_all()
+
+        # note that here we are adding commands to an existing software
         obs = qdb.software.Command.create(
             self.software, "Test Command", "This is a command for testing",
             self.parameters, self.outputs)
@@ -355,6 +362,7 @@ def test_create(self):
                          {'parameters': [], 'outputs': [],
                           'ignore_parent_command': False})
 
+        # here we are creating a new software that we will add new commads to
         obs = qdb.software.Command.create(
             self.software, "Test Command 2", "This is a command for testing",
             self.parameters, analysis_only=True)
@@ -426,6 +434,22 @@ def test_create(self):
                'ignore_parent_command': False}
         self.assertEqual(obs.merging_scheme, exp)
 
+        # now that we are done with the regular creation testing we can create
+        # a new command with the name of an old deprecated command and make
+        # sure that is not deprecated now
+        # 1. let's find the previous command and make sure is deprecated
+        cmd_name = 'Split libraries FASTQ'
+        old_cmd = [cmd for cmd in self.software.commands
+                   if cmd.name == cmd_name][0]
+        self.assertFalse(old_cmd.active)
+
+        # 2. let's create a new command with the same name and check that now
+        #    the old and the new are active
+        new_cmd = qdb.software.Command.create(
+            software, cmd_name, cmd_name, parameters, outputs=outputs)
+        self.assertTrue(old_cmd.active)
+        self.assertTrue(new_cmd.active)
+
     def test_activate(self):
         qdb.software.Software.deactivate_all()
         tester = qdb.software.Command(1)