Disclaimer: I am a self taught home sewist with an interest in natural materials.  The advice that I am sharing is based on general best practices and a bit of personal experience. Hopefully it will help you think about how you sew. 

Much of the enjoyment I get from sewing comes from the materials I use.   I like the feeling of natural fiber fabric, and I personally like the way that thread made from natural fibers feels somehow a little more “alive”.  It is a subtle distinction, but I personally also prefer the way that a seam sewn with cotton thread looks.  (And the wooden spools that Scanfil uses for their thread just makes sewing feeling a little more special). 

I am also very hard on my clothing.  I wear the things I sew, and outside of a few special pieces, I wear them as part of my bike commuting, running around in the park, occasionally climbing trees, active lifestyle. So far, I have found that seams sewn with cotton thread hold up just fine, but through talking to other sewists I have come to realize that there is an idea that cotton thread is somehow difficult to sew with.  I have not found that to be the case, but I also switched to cotton thread very early in my time sewing, and there are some adjustments that my specific sewing setup forced me to make that may be helpful for other people.  So, here are a few of the things that I find helpful when sewing with cotton thread as compared to sewing with polyester thread. 

When sewing with cotton thread the thing to remember is that it doesn’t stretch, and it is weak enough that it can often by snapped simply by pulling on it.   Much of the difference between sewing with cotton thread and polyester thread comes down to reducing the stress on your thread, both during sewing and while wearing the garment. 

Despite being a little more delicate to sew with, I have found that cotton thread holds up about as well as the fabric does. For example:

The above pants were sewn with Scanfil Organic Cotton thread in 50/2 weight (not the heavier, recommended-for-trousers 30/2 weight) and are over three years old. There are a few places where the thread has worn through and the seams will need to be re-sewn, but in this case the 8oz cotton twill fabric needed repair long before I started having problems with the seams.

Suggestions, in no particular order:

Reduce the stress:

Decrease the stitch length.  More stitches per centimeter leads to less strain on any individual stitch.   More stitches in a shorter amount of seam also distributes any stretching force across more stitches and more fabric, giving the seam a little more spring that doesn’t rely on the ability of the thread to stretch.  A shorter stitch length does mean that sewing a seam takes longer – there is a reason that fast fashion uses longer stitch lengths, but I like sewing, so taking a little longer on a seam is not a problem. 

Practice sewing smoothly.  Sudden sharp increases in speed can put extra stress on the thread, and if there is any extra friction in the system, this can cause the thread to snap.

Generally good sewing habits that become a little more important when using cotton thread:

Match thread to needle:  if the eye of the needle is a little too small, it can create extra friction and strain on the thread, leading to the thread snapping (among other problems). 

Double check your tension: Cotton thread is spun from many short fibers (even long staple cotton is “short” when compared to polyester) which means that it will move through your machine differently than polyester thread.  I generally work with a scrap of fabric from the project I am working on, until the stitch length and tension work well together. 

Even good cotton thread will leave more lint in your machine when compared to polyester thread.  Between projects I make a habit of brushing out all the places that lint tends to build up.

Advanced level changes  

(These are not necessary for successful sewing with cotton thread, but to my mind they make sewing more interesting)

Think about your seams or what seam options your pattern calls for.  French seams or lapped seams are great for redistributing strain.  Bonus, they create a clean inside finish, with no need for an overlocker or zig-zag stitch. 

Think about how difficult it might be to re-sew a seam later if it does wear through.  If possible, re-think the sewing order in high stress areas to make later re-sewing easier. 

For all that sewing with cotton thread can take a little more thought and practice when compared to polyester, I find that it is entirely worth the effort.