diff --git a/code/ATMOSPHERICS/components/omni_devices/filter.dm b/code/ATMOSPHERICS/components/omni_devices/filter.dm
index 56171a0880..00e2f9d5dc 100644
--- a/code/ATMOSPHERICS/components/omni_devices/filter.dm
+++ b/code/ATMOSPHERICS/components/omni_devices/filter.dm
@@ -33,8 +33,10 @@
 	return ..()
 
 /obj/machinery/atmospherics/omni/atmos_filter/sort_ports()
+	var/any_updated = FALSE
 	for(var/datum/omni_port/P in ports)
 		if(P.update)
+			any_updated = TRUE
 			if(output == P)
 				output = null
 			if(input == P)
@@ -50,6 +52,8 @@
 					output = P
 				if(ATM_O2 to ATM_N2O)
 					atmos_filters += P
+	if(any_updated)
+		rebuild_filtering_list()
 
 /obj/machinery/atmospherics/omni/atmos_filter/error_check()
 	if(!input || !output || !atmos_filters)
@@ -231,7 +235,6 @@
 		target_port.mode = mode
 		if(target_port.mode != previous_mode)
 			handle_port_change(target_port)
-			rebuild_filtering_list()
 		else
 			return
 	else
diff --git a/html/changelogs/Meghan Rossi - fix omni filters.yml b/html/changelogs/Meghan Rossi - fix omni filters.yml
new file mode 100644
index 0000000000..595dd331e7
--- /dev/null
+++ b/html/changelogs/Meghan Rossi - fix omni filters.yml	
@@ -0,0 +1,4 @@
+author: Meghan-Rossi
+delete-after: True
+changes: 
+  - bugfix: "Fixed omni filters reacting incorrectly to configuration changes that swap ports."
\ No newline at end of file