I guess the OP opens a new emacs instance, which might be loading agenda files each time on initialization?

If that is the case, emacsclient is probably the solution. or Open files in a new frame.

John

-----------------------------------
Professor John Kitchin 
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803

On Wed, Mar 2, 2016 at 1:41 PM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
On Thursday,  3 Mar 2016 at 01:46, Louis Turk wrote:
> Hi everyone,
>
> I use emacs all day long for many purposes, including programming. I
> open emacs with org-mode on one desktop, and leave it running
> continually. I do not want emacs to load the org-agenda files every time
> I open a source-code file, but rather only when I open a file with the
> .org extension. How can this be done?

Why would your agenda files get loaded whether you visit an org file or
any other file?  You must have customised something that opens those
files as the default behaviour is to open them only if you invoke one of
the agenda commands.
--
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.91.1, Org release_8.3.4-626-gb62d55