Exercise is great for you in so many ways but ultimately it is a stress on your body. The goal with any training program should be to improve performance, reduce weight, build muscle, and/or increase strength without causing injury. If done right you can limit your risk of injury. There are several things you can do to remain injury free. When beginning an exercise program you should get into it slowly. Most people are far too overzealous and do too much initially. Take your time and start slowly don't be in a hurry. It took you a while to get out of shape it will take a while to get back into shape. If you go too fast you will likely get injured. If you are beginning a running program start with a walk/run. If you have never ran then a good ratio is 4 minutes walking 1 minute jogging doing this 20 minutes to start 3-4 days a week. Increase your time no more than 10% each week and include recovery weeks roughly every 4 weeks. You can follow the same ratios for most other exercise programs. Most people are so excited to begin a program they forget to include the important things like stretching, massage, and foam rolling. These things are an essential part of your exercise program and should not be overlooked. Prior to your workout it is beneficial to do some active or moving stretches. Static stretches are best to complete when your workout is done. If you are going to use the foam roll it is best done before a workout or after (before you do static stretching). Deep tissue massage can be very helpful to keep your body healthy and injury free. It is best done on a regular basis 1 to 2 times a month depending on your exercise load. If you schedule a deep tissue massage it should be scheduled like a workout. Don't get a deep tissue massage on day that you have a tough workout.
Listening to your body is important when you are training for any event or when you begin an exercise program. If you start to feel a pain that does not go away in a few days then you should take action. Finding a good chiropractor can be essential to keeping you injury free. Look for a chiropractor that can also perform ART (active release therapy) and Graston. Both ART and Graston manipulate tissue in ways you can't get from a deep tissue massage. The Graston tools can also get into small areas that you couldn't get to in a massage. Look for a Chiropractor that has a lot of experience working with athletes.
If you have done everything right and you still get injured then think about what you can do not what you can't do! If you are a runner you have a few alternatives to running you could try. If I have a runner who is injured and can't run then I will have them either do either deep water running or the elliptical. Deep water running is a great alternative to running without any impact! If you are a person who is prone to injury then deep water running can be added to your training program in place of one of your weekly shorter runs. There are always alternatives and ways that you can keep moving. Good luck, train hard, have fun and keep moving!