diff --git a/src/core/qgsproject.cpp b/src/core/qgsproject.cpp
index 3c00d78b71e..0d8dddf698d 100644
--- a/src/core/qgsproject.cpp
+++ b/src/core/qgsproject.cpp
@@ -428,6 +428,7 @@ void QgsProject::setCrs( const QgsCoordinateReferenceSystem &crs )
   writeEntry( QStringLiteral( "SpatialRefSys" ), QStringLiteral( "/ProjectCRSProj4String" ), crs.toProj4() );
   writeEntry( QStringLiteral( "SpatialRefSys" ), QStringLiteral( "/ProjectCRSID" ), static_cast< int >( crs.srsid() ) );
   writeEntry( QStringLiteral( "SpatialRefSys" ), QStringLiteral( "/ProjectCrs" ), crs.authid() );
+  writeEntry( QStringLiteral( "SpatialRefSys" ), QStringLiteral( "/ProjectionsEnabled" ), crs.isValid() ? 1 : 0 );
   setDirty( true );
   emit crsChanged();
 }
diff --git a/src/core/qgsprojectfiletransform.cpp b/src/core/qgsprojectfiletransform.cpp
index 60f229cd3be..8dfa152643b 100644
--- a/src/core/qgsprojectfiletransform.cpp
+++ b/src/core/qgsprojectfiletransform.cpp
@@ -617,28 +617,128 @@ void QgsProjectFileTransform::transform2200to2300()
 
 void QgsProjectFileTransform::transform2990()
 {
-  QDomNodeList srsNodes = mDom.elementsByTagName( QStringLiteral( "SpatialRefSys" ) );
+  // transform OTF off to "no projection" for project
+  QDomElement propsElem = mDom.firstChildElement( QStringLiteral( "qgis" ) ).toElement().firstChildElement( QStringLiteral( "properties" ) );
+  QDomNodeList srsNodes = propsElem.elementsByTagName( QStringLiteral( "SpatialRefSys" ) );
+  QDomElement srsElem;
+  QDomElement projElem;
   if ( srsNodes.count() > 0 )
   {
-    QDomElement srsElem = srsNodes.at( 0 ).toElement();
-    QDomNodeList projNodes = srsElem.elementsByTagName( "ProjectionsEnabled" );
+    srsElem = srsNodes.at( 0 ).toElement();
+    QDomNodeList projNodes = srsElem.elementsByTagName( QStringLiteral( "ProjectionsEnabled" ) );
     if ( projNodes.count() == 0 )
     {
-      QDomElement projElem = mDom.createElement( QStringLiteral( "ProjectionsEnabled" ) );
-      projElem.setAttribute( "type", "int" );
-      projElem.setNodeValue( "0" );
+      projElem = mDom.createElement( QStringLiteral( "ProjectionsEnabled" ) );
+      projElem.setAttribute( QStringLiteral( "type" ), QStringLiteral( "int" ) );
+      QDomText projText = mDom.createTextNode( QStringLiteral( "0" ) );
+      projElem.appendChild( projText );
       srsElem.appendChild( projElem );
     }
   }
   else
   {
-    QDomElement srsElem = mDom.createElement( QStringLiteral( "SpatialRefSys" ) );
-    mDom.appendChild( srsElem );
-    QDomElement projElem = mDom.createElement( QStringLiteral( "ProjectionsEnabled" ) );
+    srsElem = mDom.createElement( QStringLiteral( "SpatialRefSys" ) );
+    projElem = mDom.createElement( QStringLiteral( "ProjectionsEnabled" ) );
     projElem.setAttribute( "type", "int" );
-    projElem.setNodeValue( "0" );
+    QDomText projText = mDom.createTextNode( QStringLiteral( "0" ) );
+    projElem.appendChild( projText );
     srsElem.appendChild( projElem );
+    propsElem.appendChild( srsElem );
   }
+  // transform map canvas CRS to project CRS - this is because project CRS was inconsistently used
+  // prior to 3.0. In >= 3.0 main canvas CRS is forced to match project CRS, so we need to make
+  // sure we can read the project CRS correctly
+  QDomNodeList canvasNodes = mDom.elementsByTagName( QStringLiteral( "mapcanvas" ) );
+  if ( canvasNodes.count() > 0 )
+  {
+    QDomElement canvasElem = canvasNodes.at( 0 ).toElement();
+    QDomNodeList projectionsNodes = canvasElem.elementsByTagName( QStringLiteral( "projections" ) );
+    bool hasOtf = false;
+    if ( projectionsNodes.count() > 0 )
+    {
+      QDomElement projectionsElem = projectionsNodes.at( 0 ).toElement();
+      hasOtf = projectionsElem.text().toInt();
+    }
+
+    QDomNodeList canvasSrsNodes = canvasElem.elementsByTagName( QStringLiteral( "spatialrefsys" ) );
+    if ( canvasSrsNodes.count() > 0 )
+    {
+      QDomElement canvasSrsElem = canvasSrsNodes.at( 0 ).toElement();
+      QString proj;
+      QString authid;
+      QString srsid;
+
+      QDomNodeList proj4Nodes = canvasSrsElem.elementsByTagName( QStringLiteral( "proj4" ) );
+      if ( proj4Nodes.count() > 0 )
+      {
+        QDomElement proj4Node = proj4Nodes.at( 0 ).toElement();
+        proj = proj4Node.text();
+      }
+      QDomNodeList authidNodes = canvasSrsElem.elementsByTagName( QStringLiteral( "authid" ) );
+      if ( authidNodes.count() > 0 )
+      {
+        QDomElement authidNode = authidNodes.at( 0 ).toElement();
+        authid = authidNode.text();
+      }
+      QDomNodeList srsidNodes = canvasSrsElem.elementsByTagName( QStringLiteral( "srsid" ) );
+      if ( srsidNodes.count() > 0 )
+      {
+        QDomElement srsidNode = srsidNodes.at( 0 ).toElement();
+        srsid = srsidNode.text();
+      }
+
+      // clear existing project CRS nodes
+      QDomNodeList oldProjectProj4Nodes = srsElem.elementsByTagName( QStringLiteral( "ProjectCRSProj4String" ) );
+      for ( int i = oldProjectProj4Nodes.count(); i >= 0; --i )
+      {
+        srsElem.removeChild( oldProjectProj4Nodes.at( i ) );
+      }
+      QDomNodeList oldProjectCrsNodes = srsElem.elementsByTagName( QStringLiteral( "ProjectCrs" ) );
+      for ( int i = oldProjectCrsNodes.count(); i >= 0; --i )
+      {
+        srsElem.removeChild( oldProjectCrsNodes.at( i ) );
+      }
+      QDomNodeList oldProjectCrsIdNodes = srsElem.elementsByTagName( QStringLiteral( "ProjectCRSID" ) );
+      for ( int i = oldProjectCrsIdNodes.count(); i >= 0; --i )
+      {
+        srsElem.removeChild( oldProjectCrsIdNodes.at( i ) );
+      }
+      QDomNodeList projectionsEnabledNodes = srsElem.elementsByTagName( QStringLiteral( "ProjectionsEnabled" ) );
+      for ( int i = projectionsEnabledNodes.count(); i >= 0; --i )
+      {
+        srsElem.removeChild( projectionsEnabledNodes.at( i ) );
+      }
+
+      QDomElement proj4Elem = mDom.createElement( QStringLiteral( "ProjectCRSProj4String" ) );
+      proj4Elem.setAttribute( QStringLiteral( "type" ), QStringLiteral( "QString" ) );
+      QDomText proj4Text = mDom.createTextNode( proj );
+      proj4Elem.appendChild( proj4Text );
+      QDomElement projectCrsElem = mDom.createElement( QStringLiteral( "ProjectCrs" ) );
+      projectCrsElem.setAttribute( QStringLiteral( "type" ), QStringLiteral( "QString" ) );
+      QDomText projectCrsText = mDom.createTextNode( authid );
+      projectCrsElem.appendChild( projectCrsText );
+      QDomElement projectCrsIdElem = mDom.createElement( QStringLiteral( "ProjectCRSID" ) );
+      projectCrsIdElem.setAttribute( QStringLiteral( "type" ), QStringLiteral( "int" ) );
+      QDomText srsidText = mDom.createTextNode( srsid );
+      projectCrsIdElem.appendChild( srsidText );
+      QDomElement projectionsEnabledElem = mDom.createElement( QStringLiteral( "ProjectionsEnabled" ) );
+      projectionsEnabledElem.setAttribute( QStringLiteral( "type" ), QStringLiteral( "int" ) );
+      QDomText projectionsEnabledText = mDom.createTextNode( hasOtf ? QStringLiteral( "1" ) : QStringLiteral( "0" ) );
+      projectionsEnabledElem.appendChild( projectionsEnabledText );
+      srsElem.appendChild( proj4Elem );
+      srsElem.appendChild( projectCrsElem );
+      srsElem.appendChild( projectCrsIdElem );
+      srsElem.appendChild( projectionsEnabledElem );
+
+      QDomNodeList srsNodes = propsElem.elementsByTagName( QStringLiteral( "SpatialRefSys" ) );
+      for ( int i = srsNodes.count(); i >= 0; --i )
+      {
+        propsElem.removeChild( srsNodes.at( i ) );
+      }
+      propsElem.appendChild( srsElem );
+    }
+  }
+
 
   QDomNodeList mapLayers = mDom.elementsByTagName( QStringLiteral( "maplayer" ) );