Diesel Tuner's Blog

The First 4 Upgrades To Do On 3rd Gen 5.9L Cummins

Posted by Ben Lawson on Aug 23, 2022 9:32:29 AM





These are the first 4 upgrades you should make to your 2003-2007, 5.9L Cummins.

If you're just getting into the diesel game with a third-generation Cummins 5.9L you're on the right track. While people say the 12v motors are great for being able to handle lots of power and having lots of upgrades. The 24v is also a very solid choice for both of those same reasons. With more hp from stock than the 12v motors and some beefy internals, like forged rods that can handle over 800hp. There is lots of potential to be had. 

Red 3rd Gen Cummins on Dyno

It's a great truck from the factory, but if you're anything like the rest of us you're not interested in keeping it stock. Especially with the number of bolt-on upgrades available for the 5.9L. Why not make a great truck even better? Today we will show you the first 4 mods you should do to your 5.9L Cummins turbo diesel. 


Before you start your modifications it's always a good idea to:

  • Check for boost leaks
  • Make sure all engine codes are dealt with
  • Do a leak down test to check compression
  • Have an end goal for horsepower or torque 


Stealth Boost Tester


1) Aftermarket Intake 

One of the best mods to get on the truck right away is a cold air intake. The stock cold air intake is lacking, from the way it seals to the mildly restrictive airflow and filter. Let's just say there's a bit of room for improvement. And with so much room to improve any after-market intake on the market should be an improvement. Some of the brands we recommend considering are S&B, Wehrli Custom Fab, and AFE. They all improve on multiple parts of the intake system that will ensure better performance for the 5.9. 


Cold air intakes will reduce the amount of work the engine has to do when intaking air thanks to the less restrictive flow. Along with improving the intake air temperatures by sealing better. Sucking in less hot air from under the hood. Taking less effort to suck in the air will improve the engine's efficiency and in turn provide more power and better fuel economy. Cooler intake air temps also mean more air is entering the combustion chamber volume. Which should give you more power and a cleaner burn. Cold air intakes are not only on the more affordable side of upgrades you'll want to do to your truck. They are also very easy to install which makes them a great first place to start when modifying your truck. 


2) Tuning 

06 cummins on dyno

Tuning is the most cost-effective way to bring your diesel truck to life. If you're starting stock, tuning will get you the most horsepower out of any mod you can install. Plus if you have any other bolt-on upgrades installed like a cold air intake. A custom tune will bring out the maximum potential of those mods as well. Stock or modified, custom tuning is always what you'll want. It can bring out the maximum performance your engine has to offer. Along with providing the best overall design and support to keep your truck operational if something goes wrong. Another important reason to go custom is the ability to utilize switch-on-the-fly tuning. This allows the driver to switch through multiple different custom tunes while driving. Tunes can either provide you with tons of extra power while sacrificing fuel efficiency and EGTs or provide you with great fuel efficiency while sacrificing some power. You can see how it's not always a best of both worlds situation and that's why you'll want to go with a company that offers switch-on-the-fly custom tuning even if you're going with a single tune. Because you may and most likely will want to upgrade in the future. 


Learn More About Cummins EZ Lynk Tuning


Our favorite devices to use for installing custom tuning are the MM3 if you have an 03-05 Cummins because of the great compatibility or if you have an 06-07 Cummins we highly recommend using EFI Live due to the added features and benefits their product will be able to offer for your truck. Another option some choose to go with is tuning boxes. These stay plugged into the truck while driving and trick the ECU into sending more fuel into the cylinders which can have the potential to create more power. This is not a true way of tuning your truck and will not have anywhere near the effect that a custom tune does. We highly recommend staying away from these types of tuners even with the price efficiency considered. With a proper custom tune, you can expect to see up to 100 extra horsepower and 180 extra pound-feet of torque out of a completely stock motor.  


3) Transmission 


Cummins Transmission Install 3The stock transmissions that come with the Cummins 5.9L are a major weak link when trying to build these trucks to handle major power. The stock automatic is able to handle about 400 horsepower before it starts slipping and the clutch that comes with the manual transmission isn't able to handle much more than that either. So if you plan to push your truck past 400hp, which we know can easily be done. Then upgrading to a built transmission is something you are going to want to do. Sadly this modification doesn't have the potential to add that much power and is relatively costly. However, it is a very necessary upgrade for any Cummins owner looking to go fast and put down some real power. 


4) Turbos 

Cummins Stealth Shot-1

The stock turbo in the third generation of 5.9L Cummins engines is a great performer when it comes to stock power levels. However, it often starts to suffer at higher power levels where it starts to run out of air at the top of the rev range. We've dyno'd the stock 5.9L Cummins with just a tune installed and were able to get about 400hp and 720 pound-feet of torque out of the engine before the turbo wasn't able to keep up with the rate of air being consumed by the engine and horsepower started to drop. This means that upgrading the turbo is a must if you want to see anywhere north of 400hp or 720 pound-feet of torque. Luckily dropping in a larger turbo is pretty easy and it will easily get you into much higher horsepower figures with just a tune. To give you an idea of what kind of power you can get out of a turbo upgrade. Calibrated Power tested their Stealth 67 turbo on a 2006 Cummins sporting 100% over Exergy Injectors with a 12mm Exergy Cp3 pump. The truck made over 800 RWHP. Now you won't be seeing that kind of power without installing some other supporting mods but the point is that upgrading the turbo can go a very long way in reaching those kinds of numbers and is ultimately a limiting factor when it comes to breaking past 400hp with a stock engine. The great thing about upgraded turbos is that they will give you greater peak power across the entire operating range. Installing the turbo alone will only net you around 30-40hp though and that's why we've listed this modification 4th in our list. You will need custom tuning in order to get actual performance out of an upgraded turbo. Along with a built transmission to handle the extra power you'll be adding. 


700HP Capable Drop-In Stealth 64, 5.9L 


Here are some things to consider when upgrading to a larger turbo:


  • What is your end goal for hp? 
  • Where in the rev range do you want the power to be?
  • Is upgrading to a twin kit a possibility in your future?
  • Custom tuning is a must
  • Having a built transmission is a must



Overall, While they do have a few shortcomings, the second generation of Cummins 5.9L engines are a great platform to build for more power. With so many modifications on the market, it's practically impossible to keep the truck stock. So since it's only a matter of time before the modifications begin on your truck. We wanted to start you off on the right foot with this list of the first 4 modifications you should do to your 5.9L Cummins. We hope it gave you some good insight into what's worth upgrading on your truck. If this information was useful be sure to check out the links below for more helpful information on the second-generation Cummins 5.9L.


Most Popular Cummins Articles: 

1,000 HP Single Turbo 5.9L Cummins Daily Driver

2006 Cummins

The History of The 5.9L Cummins

Cummins 5.9 history

Topics: EFILive, Cummins, Cummins Turbo, Cummins Diesel, Diesel Tuning, 2003 Cummins Tuning, 2006 Cummins Tuning, 2004 Cummins Tuning, 2005 Cummins Tuning, Cummins Tuning, 2004.5 Cummins