diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7a5c250c8b..7ff1706cfd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -40,6 +40,7 @@ release.
 - Skypt has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5443](https://github.com/USGS-Astrogeology/ISIS3/issues/5443)
 
 ### Fixed
+- Fixed bug in which not all references to 'version' file were replaced with new 'isis_version.txt' file [#5374](https://github.com/DOI-USGS/ISIS3/issues/5374)
 - Fixed a bug in which the IrregularBodyCameraGroundMap unit test was removed but not the associated truth file. [#5461](https://github.com/DOI-USGS/ISIS3/issues/5461)
 - Fixed a bug in which the histogram tool used the entire image to calculate bin size, which caused an issue with high dynamic range images. [#5371](https://github.com/DOI-USGS/ISIS3/issues/5371)
 - Fixed a bug in which 'version' file was compiled as source and prevented subsequent ISIS recompilation [#5374](https://github.com/DOI-USGS/ISIS3/issues/5374)
diff --git a/isis/config/config.mak b/isis/config/config.mak
index 750755bd0b..686bbc7a00 100644
--- a/isis/config/config.mak
+++ b/isis/config/config.mak
@@ -5,7 +5,7 @@
 SHELL=bash
 .SILENT:
 
-ISISLOCALVERSION := $(shell head -n 3 $(ISISROOT)/version | tail -n 1 | sed 's/\#.*//' | sed 's/ *$$//')
+ISISLOCALVERSION := $(shell head -n 3 $(ISISROOT)/isis_version.txt | tail -n 1 | sed 's/\#.*//' | sed 's/ *$$//')
 QMAKE ?= $(shell which qmake 2 >& /dev/null)
 
 ifeq ($(QMAKE),)
diff --git a/isis/scripts/isisVarInit.py b/isis/scripts/isisVarInit.py
index b3c131c50d..9cd11a06d4 100755
--- a/isis/scripts/isisVarInit.py
+++ b/isis/scripts/isisVarInit.py
@@ -64,7 +64,7 @@ def activate_text(shell: dict, env_vars: dict, cat=False) -> str:
         lines.append(shell["activate_extra"])
 
     if cat:
-        lines.append("cat $ISISROOT/version")
+        lines.append("cat $ISISROOT/isis_version.txt")
 
     return "\n".join(lines)
 
diff --git a/isis/src/base/objs/Environment/Environment.cpp b/isis/src/base/objs/Environment/Environment.cpp
index ae33d92afa..56363cf1a2 100644
--- a/isis/src/base/objs/Environment/Environment.cpp
+++ b/isis/src/base/objs/Environment/Environment.cpp
@@ -118,7 +118,7 @@ namespace Isis {
       line1 = validPartOfLine.cap();
     }
     else {
-      IString msg = "$ISISROOT/version line 1, no valid text found";
+      IString msg = "$ISISROOT/isis_version.txt line 1, no valid text found";
       throw IException(IException::Programmer, msg, _FILEINFO_);
     }
 
@@ -126,7 +126,7 @@ namespace Isis {
       line2 = validPartOfLine.cap();
     }
     else {
-      IString msg = "$ISISROOT/version line 2, no valid text found";
+      IString msg = "$ISISROOT/isis_version.txt line 2, no valid text found";
       throw IException(IException::Programmer, msg, _FILEINFO_);
     }
 
@@ -134,7 +134,7 @@ namespace Isis {
       line4 = validPartOfLine.cap();
     }
     else {
-      IString msg = "$ISISROOT/version line 4, no valid text found";
+      IString msg = "$ISISROOT/isis_version.txt line 4, no valid text found";
       throw IException(IException::Programmer, msg, _FILEINFO_);
     }