Level One: Foundation Fitness
The first phase focuses on teaching the central nervous system and the muscles to have better communication, with regard to movement. This will improve the structure of your movements, and thus increase the impact of your strikes, strengthen your movements, and help you develop much greater speed.
At this time, we'll also begin to work on building the endurance of your muscles. The main exercises used are all single joint, ground based movements, keeping it simple, and teaching the body to move in a way that will avoid the potential for long-term injuries. Just because you don't feel pain today doesn't mean you won't suffer from it later, and for the rest of your life. We'd like to avoid that.
Stage One - Motor Learning - 4-6 Weeks
Skipping this step can have adverse effects on your joins, muscles, and espectially your fitness achievements. The main focus here has to do with the way the nervous system works.
For the first few weeks of conditioning, it won't actually be muscular growth that causes an increase in strength. With the introduction of a new stimulus, the nervous and musculoskeletal systems acquire a better communication, leading to improvements in load capacity.
In other words, your body figures out what is needed, and it adapts. This is known as the "General Adaptation Syndrom."

A good coach will help you to gradually learn propper movement, through this phase, minimizing the load (weight) and difficulty, focusing only on developing propper movement before moving on to heavier loads. Just because you CAN lift it, doesn't mean you SHOULD lift it.
I often begin people with only five-pound dumbbells for dumbbell lifts. Why only 5lbs? We're building structure, and worrying about getting the weight where it has to go can be very counter-productive. The muscles and central nervous system are learning to communicate need based on stimulus.

Depending on a person's current physical conditioning, we may begin with only 1-2 sets of just a few reps, or as many as three sets of 15-20 reps. The idea is learning to move and utilize muscular strength efficiently. Rather than worrying about building muscle, we're strengthening the movements, which in turn increases your potential output. In other words - you'll get stronger.
Rest periods will vary, depending on the individual. You may need a minute between sets. You may need 3 minutes. Observe your heart rate. As it begins to drop back down, you'll start getting an idea of when you should perform the next set. Don't over do it, but also don't under do it. In time, rests will only be 30 seconds. Don't rush to the goal, just enjoy the journey.
The main exercises to focus on are those requiring stability, balance, and skill. You'll find many of these on the Structural Exercises page.
We begin with only two main exercises being taught. The primary focus is going to be on perfect form. If the form needs a lot of work, we'll continue with only those two exercises throughout a few more sessions. Once there is reasonable form, we can add one or two more exercises to the routine. This continues throughout this stage, with weight being added in the following stage.
Below you will find the lay-out for the first stage of conditioning. This is meant to help you comprehend the structure of this training, so that you can design a decent start-up program for yourself.

It is best to keep the weight minimal while pushing yourself to maintain 4 second movements. Since these movements are so slow, they really challenge your form, but with the ability to correct the movement while still moving. However, if you are practicing on your own, it can be difficult to really see the problem areas, and so bad form may become normal. This is a very bad thing. So pay careful attention to every aspect of every exercise.
The easiest way to do this is to work out with a mirror, keeping images of people performing these exercises with perfect form on the wall. It will help as a reference. There is a reason that most gyms have mirrors on at least one wall.
There are several of these exercises given on the Structural Exercises page. And while these fulfill the main requirement for the main exercises, we also must look at what is to be used as our supplemental exercises. After all, if you want a complete work out, you're going to need a lot more going on than just bench presses and leg lifts. Such exercises should be those which are simpler to perform, and this will always depend on the individual. Some examples are pull-ups, core conditioning exercises, and dips.

Putting it Together
At this point you may be wondering how all this is going to fit together into a regular training program. Of course this all depends on what you have available, whether you are solo or with a partner, and if you are only training in the fitness aspect of MMA or you are practicing technique, as well.
Fear not, however, because I am about to give you a basic protocall to follow, which you can use to design your own regular training routine, simply by switching the exercises.
What's Included in Every Workout?
General Warm Ups: These help to raise the body's core temperature while getting the heart rate up, in preparation for work. They are a handful of exercises that we use to get started, before continuing with the MMA-related warm ups.
MMA Drills: These can be considered an extension of the warm ups, but these exercises are designed to help condition our MMA techniques, both on the ground, as well as standing. The 12-count drill is a good example, or shrimping.
Main Exercises: These are those single-joint structural exercises. We only add one or two at a time. Keep the load very low at this level, because the idea here is learning to move propperly. It's not about muscle growth, yet. It's about strengthening the communication between the muscles and the brain.
Supplemental Exercises: After going through those main exercises, we want to continue the work out with some exercises that ensure we are getting a complete work out. These can include push ups, pull ups, dips, and so forth. Core conditioning is a great supplement to the main exercises.
Finisher: After a work out, there is likely to be some remaining energy left. Get rid of it! A finisher is an exercises or exercises which give you that final conditioning at the end of your workout, after you've already begged for mercy. Burpees make excellent finishers, challenging both upper and lower body strength, while also challenging your cardio.
Cool Downs: Finish every work out with something light, such as shadow boxing or bag work, and then a complete static stretching routine, to gradually bring down the heart rate and dispell metabolic waste.
Stage Two - Structural Integrity & Strength Endurance -
4-6 Weeks
"Structural integrity" means to have a strong network of connective tissue. We are not going to focus more on the core conditioning exercises, while adding a little weight to the structural exercises of before.

Stage two of the first phase is pretty straight forward. Increase the load while decreasing the rest periods. Increase the weight on single-joint exercises (isolation exercises), and begin to include more Core Conditioning Exercises, following the 3-stage protocall given.
The training schedule should include core conditioning before the structural exercises. Don't forget a good warm up and cool down.

8 - 12 Week Training Schedule (Summing it Up)
Having explained how the two stages are framed, now I will just lay out the training for these stages in a way that can be followed in an overall MMA training program. Remember, the main focus right now is learning to move correctly and building a foundation of strength. Don't get over zealous and neglect your own correction. Everyone who starts out with any fitness program lacks stability in most movements without even realizing it. If you correct this now, you're future as an MMA star will be off to a much better start. If a beautiful house has a bad foundation, it will crumble.

It looks like a long list, but most of these are short durration exercises. You should be able to get through everything here in 45 minutes or less. Also, this is only a sample that covers the concept of both stage one and stage two, just to give you an idea of how we design training programs. You should only do what you can, and make sure you're not learning bad form.
This is not meant to limit you to a single training routine. You're job is to design your own personalized training regimen, using this example as an aid to help you. Note that I've included a short core conditioning part to this routine. All exercises outside the main exercises are meant to supplement the training by developing the muscles around the main targeted muscles, to aid in developing stability.
The finisher adds a final intensity to the training. The idea is to take whatever energy you have left and put it to use. I've only included burpees here, but you cn add more, if you need to. Another great reason for a cardio-related finisher is to really get the blood pumping before the cool down, as a way to more efficiently eliminate metabolic waste.
HEY!!!
If you are going to an MMA gym a few times each week, you are going to want to focus your home training to those things which you're not already getting at the gym. For instance, I trained for a while at a gym that didn't drill the ground movements regularly, so I would add them to my routine. If, however, you are doing them regularly at the gym, just run through a short warm up routine for the main exercises, and end with flexibility exercises (static stretching). You may even be able to reduce it all to simply the main exercises and leave out everything else (except warm ups and cool downs), for now, if you are getting a decent core work out at the gym.
However, if you are not training at a gym, you'll need a complete training routine for home conditioning. But if you're just getting started, it may still be best to keep it short. Long work outs have a tendency to reduce the class size.
EXERCISE SELECTION
You may still be a little confused as to what exercises to use as your main exercises. At first, you may want to keep it entirely calisthenic, with push ups and bodyweight squats, and an exercise for the lower back (roman chair, for example). Then start adding the weight after you can easily enough perform 12 with 4-second movements (no pauses!!!). Then, the first exercises I start people out on are the big three of power lifting. Bench Press, Squat, and Deadlift. These three work all the main areas of the body. After the client has show significant improvement in form, I'll add another exercise or two, continuing in this way into level 2.
After I see good form in bench presses, I switch everyone over to dumbbell presses. This is because the dumbbells challenge stability a lot more. Even my stronger clients, when they first start, find it difficult to control their movement with 5 pound dumbbells. It's not about strength. It's about motor control.
At the same time as all of this, I am also working with each person to develop their pull ups, as this is, in my opinion, the very best exercise to perform for MMA conditioning.
So, to lay out the weight training a little more clearly...
Stage One (all exercises move at 4 secend intervals)
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bench press, reverse squat, lateral pull down
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bench press, squat, deadlift, pull ups Minimal weight for each.
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dumbbell press, squat, deadlift, pull ups Weight slightly increased. Start low with the dumbbell press.
Stage Two (lift at 3 seconds and lower at 4 seconds)
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Increase the load to be challenging for 15 reps, with 3-4 sets.
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Monday: dumbbell press, squat, pull ups.
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Wednesday: tricep push down, deadlift, pull ups.
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Friday: dumbbell press, squat, pull ups.
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After you become used to all the exercises, add more two each day.
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Monday: dumbbell press, squat, dumbbell row, pull ups
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Wednesday: tricept push down, deadlift, lunge (with light dumbbells), pull ups.
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Friday: overhead press, curl, step ups
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In the above example, I used bold letters to show which exercises were being added to the routine, so they would stand out from the ones you've already been performing. In stage one, I give an example of adding exercises twice. In stage two, the routines are divided into three-day intervals, with a few exercises added as you go along. This progression happens at the rate by which you are ready for new challenges. Master the exercise before adding weight and adding a new exercise.
And that's level one. Pretty basic. The main goal is to learn to perform every exercise perfectly, beginning with the core three exercises of power lifting, with a side emphasis on pull ups. If you struggle with pull ups, many gyms now have assistance machines for them, and you can also begin by performing pull downs. But if you have the option of doing assisted pull ups, go for those instead.