Upgrade Confluence 3.5.13 to latest version on brandnew hardware

Hi there,

We are looking to upgrade our Confluence 3.5.13 hosted on Windows server 2003 to latest version on windows server 2016. The database is Microsoft SQL. I found this tutorial https://confluence.atlassian.com/doc/upgrading-confluence-4578.html, but it seems it is for upgrading confluence on the same hardware, not on a separate one. Can you please provide a suitable tutorial for us? 

Please cc ffong@machealth.com.au if possible for your reply. 

Thank you.

Frank Fong 

6 answers

0 votes

Hi Frank,

I would recommend that you first migrate your instance to the new server in order to check that it was successful. Then you can migrate it.

Unfortunately since 3.5.13 is not supported anymore, our 5.10 document is the oldest one we have on how to do that:

Have a look at that article and make sure you're able to successfully move Confluence. Then you can perform the upgrade steps:

  1. Upgrade first from 3.5.13 to 5.0.3
  2. Then upgrade 5.0.3 to the latest version.

You'll be able to obtain those past versions from our Confluence Download Archives.

The article you linked will have all the details on how to properly migrate.

Let us know if you have any questions.

Kind Regards,

This is Jimi, Frank's colleague.

We have downloaded the installer for 3.5.13 and after extracting we do not understand how to run the application to get it running before upgrading to 5.0.3

Could you please explain the steps to install the application on the new hardware ?

On the new server, we intend to install Microsoft SQL server 2014 or 2012 to run with the 3.5.13 confluence version.

Could you please provide us with a temporary trial license of confluence  with full access to be sure that there is no limitation on our new server before transferring our existing license to the new server. this is because we are not sure if we use our license on the new hardware, it will stop the confluence on the production environment which we cannot afford.

Please find below the zip content of the 3.5.13 that we download, please advise the next steps of Action.




Kind Regards,



Hi Jimi,

I'm unsure why you are downloading 3.5.13 if you already have it installed and running on your server. From Frank's message, I believe you already have 3.5.13 installed. Is this correct? 

You will want to actually download the 5.0.3 version first since you're upgrading your existing Confluence 3.5.13. Then, once you upgrade to 5.0.3 you will upgrade to the latest version.

You can follow the article that Frank sent earlier, on how to upgrade Confluence. Please be sure to carefully read the entire article, as you don't want to miss any steps, but there were instructions on that page on How to Run the Installer

If you didn't already have 3.5.13 installed, and didn't have any existing Confluence data, then there's no need to upgrade anything, and you can just install from the latest Confluence version. You will want to consult your Server Administrator for more information.

Regarding your MS SQL Server, I can tell you for sure that MS SQL 2014 is not supported in 3.5.13. We no longer have documentation on what is supported in 3.5.* since that version has already reached End of Life. As of 5.3* only 2008, 2008 R2, and 2012 were supported. If you use 2012 with 3.5.* you may run into issues.

Kind Regards,

Jimi - One more thing;

You can generate an Evaluation license from my.atlassian.com. Let us know if you have any trouble.

Kind Regards,

Jimi - Apologies, I remember now that you said you wanted to migrate to a new server, so yes, you can download 3.5.13 on the new server.

Follow the Confluence Installation Guide on how to install. Only 2005 /2008 /2008 RS versions of MS SQL were supported. I have been able to confirm that here:

Confluence Supported Platforms 3.5

You will want to ensure you have the supported platform ready on the new server, so please make a note of the Java version as well. Your Server Admin should be able to assist with this.

Kind Regards,

Hi Shannon,

Thank you for your reply. 

I have downloaded Confluence 3.5.13 and followed below guide on our new server: 


I was able to reach step 5 in the installation guide even though http://localhost:8080/ is not reachable because the webservice is not running yet. 

We have set up SQL Server 2008 R2 Express installed on the new confluence server, do we still need to do more configuration with the database for the SQL Server ? if yes please advise what to do.

Should we progress to level 7 in the installation guide ?

Please find below screen shots of what we have done:

Hi Shannon,


Can you please respond to my request ? 


Kind Regards,


it is urgent

Ann Worley Atlassian Team Nov 07, 2017

I am afraid SQL Server Express is not a supported platform for Confluence 3.5.x: Supported Platforms If this is to be your new Production instance, please use MS SQL Server. Here are the setup instructions for the database for Confluence 3.5: Database Setup for SQL Server

Per the screen shots it looks like you have JAVA_HOME set and are ready to proceed on that front.

Hi Ann,

Thank you for your prompt reply.

On our old confluence server, we are using SQL Server 2005 Express Edition and it is working perfectly fine.(please see below screenshots)

Now we have a new confluence sever running SQL Server 2008 R2 Express Edition. 

Shall we proceed with the setup instructions for the database for Confluence 3.5: Database Setup for SQL Server on the new confluence sever  ?

Hi there,

As Ann mentioned, Express Edition is not supported. The Supported Platforms page versions refer only to MS SQL Server. Despite it having worked before, it has not been developed for use with Express Edition, meaning there could be major issues in the future.

You will want to change to MS SQL (non-express) and try the setup that way. You also can try using another database that is supported, such as MySQL or Postgres.

Let us know if you have any questions.

Kind Regards,

Hi Shannon,

Thank you for your reply. 

We literally want to use the database temporarily to install Confluence 3.5 version then change it during our migration to the latest version of confluence.

Should we set up our confluence server for evaluation or production ? 

If we generate an evaluation license for the purpose of upgrade, does it have any limitation in data migration between our old confluence database to the new database on the new confluence server ? 

Or if we retrieve our license key from our old production confluence server, does it allow for double servers to run confluence on the same license or it will affect the old confluence server (which we do not want) ?

  • We are also at the point of exporting data from our old confluence database to the new confluence database, should we follow the standard SQL database migration or their are more steps required in the data migration ? if yes, can you provide us with the guide for database migration ?

You should follow the instructions for a standard SQL database migration.

Take your 3.5 install and export it to xml.  Move it over to a supported database for 3.5 (See https://confluence.atlassian.com/display/CONF35/Supported+Platforms )

You do not need to worry about the evaluation licence.  All they do is "time bomb" - when they expire, they just shut down functions.  Before expiry, they allow access to all functions.

Thanks, Nic, for following up! :) 

@IT Support What Nic said is correct, you can follow the standard SQL Migration article in order to migrate the database. The evaluation license does give you the same functionality as Production, and you only need to make sure to upgrade it before it expires. 

Let us know if you have any further questions.

We will be in touch if we have more questions to ask. Thank you

When we try to start confluence automatically on a windows service we encounter an error. Please what could be possible reason for this, check below screenshot:

Please note that firewall is disabled.


First, please try:

java -version


echo %JAVA_HOME%

Following with:

echo %JRE_HOME%

This will let us know your Java version, where your Java home is set, and finally the JRE home.

Please send us the results of these commands, as we need to verify them.

If you don't get results from any of the commands, please review Setting the JAVA_HOME documentation to ensure that Java home is set correctly.

Once JAVA_HOME and JRE_HOME is set you can try to start Confluence manually (not as a service):

  • To start Confluence run <installation-directory>\bin\start-confluence.bat
  • To stop Confluence run <installation-directory>\bin\stop-confluence.bat

We recommend running Confluence with a dedicated user account. To do this, use use the runas command to execute start-confluence.bat.

> runas /env /user:<DOMAIN>\<confluence> start-confluence.bat

Where <DOMAIN> is your Windows domain or computer name and <confluence> is the name of your dedicated user.

If you have any problems, send us the output of the Tomcat window here.

If everything works here, you can try to start as a service again. If you run into a problem there, then you will need to recreate the service and try again.

Kind Regards,

We could start confluence manually which was no problem at all, we actually thought it was necessary to complete step 9 of the installation guide below:


I have attached the requested screenshoots and also to show you that confluence is working manually.

My questions are:

Confluence is running fine manually not as a service, we were able to resolve the issue of the tomcat services not starting by using tomcat 7 with 64 bits, the service is now running but confluence is no more working when we run as a service, it keeps loading without result .

Please how do we resolve this issue ?

Can a support person respond to my request ? 

According to your documentation, After running service.bat install confluence. the service will be called Atlassian Confluence and will be configured to start automatically but there is none present in windows service. 


I'm moving your case to our support system because I think it will be easier to follow there. I used the support email address from this account, so please check that account for the ticket number so you can login and receive our updates.

If you have a particular email address you want me to add on the case please let me know.

Kind Regards,

Hi Shannon, 

The support email is good and at the same time, please also add below email:





Thanks, Jimi. You didn't have an Atlassian ID yet so I sent you an invite and added the user to the case.

Kind Regards,


Hi Shannon, 

I think James is not aware that our organisation has a commercial license with support access valid till Feb 28, 2918.

I think he thought we do not have a license. 


Please see below license information:

 Organisation Pen CS Pty Ltd
Date Purchased Feb 28, 2017
License Type Confluence: Commercial Server
Licensed Users 50 (25 signed up currently)

Support Period Your commercial Confluence support and updates are available until Feb 28, 2018.
Support Entitlement Number SEN-6812261
Server ID BWCM-QHEE-CFRB-OV6I (Atlassian sales or support may ask you to provide this ID)

Could you please request James to treat this as urgent. 

Thank you

Hi Jimi,

I see that you updated your case with James with the same information, and he has written you back a few hours ago, so please feel free to have a look at that and let him know if you have any questions.

Kind regards,


Hi Shannon,

I have replied James email. 

Thank you 




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