Installing MegaSquirt in Parallel With the Stock ECU

While there are many cars where MegaSquirt can completely replace the stock ECU, on some cars you’ll need to leave the stock ECU in place. There’s several reasons why you might want to do this. On some installations, you might want to have the MegaSquirt control just the fuel and would rather not deal with having to tune the ignition. Or you may have an ECU that controls the automatic transmission, has the voltage regulator for the alternator inside it, controls a drive by wire throttle, or has other features that aren’t easy to control with MegaSquirt. On a car like that, the solution is what’s called a parallel installation.

The whole idea behind a parallel installation is letting the MegaSquirt take control of what you’d like it to control (the fuel injectors and ignition system most commonly) without interfering with other systems that the factory ECU may control that may or may not really be engine management related. Sometimes this approach is called a piggyback, but that can cause a bit of confusion with systems like the Apex’i SAFC, which modifies signals to or from the stock computer. The MegaSquirt does not change any signals; instead, it will take over functions of the stock ECU outright.

Installing the MegaSquirt in parallel amounts to disconnecting the stock ECU from what you need to tune, and connecting these things to the MegaSquirt instead. You can do this with injectors, coils, IAC valves, and most anything the MegaSquirt can control. Often the toughest issue is what to do about sensors. These guidelines will help you deal with the sensors the MegaSquirt needs.


Sharing Sensors (or not)

MAP sensor: The MegaSquirt EMS has it’s own dedicated MAP sensor built in, so you will just need to add an extra vacuum line for it.

Throttle position sensor: Check the TPS signal running to the stock ECU with a volt meter. If it never goes above 5 volts, and if its voltage increases as the throttle opens, you can use this sensor with MegaSquirt. Just splice the Megasquirt TPS signal wire in to the signal wire to the stock ECU. You should not try connecting the Megasquirt’s VREF wire to the TPS, as tying two VREF signals together can cause problems.

Temperature sensors: These are a bit problematic. On some ECUs, like the early Miatas, it is possible to get the MegaSquirt and the stock ECU to both use the same sensor. To do this, you will need to remove the R4 and R7 bias resistors from the MegaSquirt and determine the bias resistors the stock ECU uses, then calibrate the MegaSquirt appropriately. This link provides more detailed information about how to share temperature sensors between the MegaSquirt and stock ECU. On some ECUs, like most GM computers, you cannot share temperature sensors with the stock ECU at all. IF your unsure of what to do here, your safest option is to provide the MegaSquirt with its own CLT and IAT sensors, separate from the stock CLT/IAT sensors that the factory ECU will continue to use.

Crankshaft position sensor / camshaft position sensor: These are sensors you can usually share with the stock ECU, but there are a few issues that can cause the MegasSquirt to not play nice with them. If you have a VR sensor and you connect the sensor to the MegaSquirt backwards, you could possibly ground the sensor and wipe out its signal. Solution– don’t wire it backwards! With Hall effect or optical sensors, sometimes the combination of pull up resistors in the MegaSquirt and stock ECU can interfere with each other. If this happens, one or both of the ECUs will not get an RPM signal. Often, you can solve this by removing the pull up resistor from the MegaSquirt.

Oxygen sensor: It’s perfectly OK to share narrow band oxygen sensors with the stock ECU. However, there’s a good chance you will want to add a wideband O2 sensor at some point, in order to give the MegaSquirt more tuning information. These often don’t work with stock ECUs, so your best bet is to weld in a second bung for the wideband sensor. Another case where it pays to have separate sensors for the MegaSquirt and the stock ECU.

So what have you really done here?

Basically, your goal in the above is to make sure that both the stock ECU and the MegaSquirt EMS have the INPUTS they need from all the necessary sensors so they can both independently make all of the calculations needed to control your engine.  Both systems ‘think’ they are in control of the engine, as they are processing all of the incoming information from these sensor inputs, and they are sending the corresponding OUTPUT signals in the way of fuel injector pulsewidths and ignition pulses.  So which one gets control of your engine now?  Well… that’s completely up to you now: which set of outputs did you actually wire up to your fuel injectors and ignition system?  That’s the system that’s controlling your engine; the other system just continues thinking it’s controlling the show when the MegaSquirt ECU is really pulling all the strings.

What if you get a Check Engine Light?

In many cases, the stock computer will continue to be dumb enough to never notice you cut it’s injector and ignition outputs.  It doesn’t like its sensor inputs cut, but it’s outputs it’s not so picky about.  In some cases, the stock computer might be smart enough to figure out that you’ve done something tricky here and it might trigger a check engine light.  In some cases it may not matter as it often wouldn’t affect performance and you should only be implementing a system like this on a off road/race use vehicle anyways, where the CEL was of no other concern.  But there are situations where this could affect performance, so you’d need to resolve the situation.  When a stock ECU activates a CEL, it often enters a ‘limp-home mode’.  If the stock ECU had control of your fuel and ignition, this would generally trigger conservative fuel and ignition maps to be used which would reduce performance.  That’s very likely not the issue here though, as you’ve got your MegaSquirt EMS in parallel controlling the fuel and spark.  But, that stock ECU may still have control of a variable intake system, or variable valve timing system, or throttle by wire system, and these could therefore also be affected by the stock ECU entering a limp-home mode restricting performance.  So this CEL can still be a problem for you.  So you basically need to determine the cause to the CEL and ‘trick’ the stock ECU into thinking everything is OK.  The right way to do this is to read the codes the stock ECU is storing to see what it’s complaining about and then resolving the issue(s).  Is it complaining that the injectors are disconnected?  You can connect dead injectors to it’s outputs to trick it– or better yet, high wattage (50w) resistors of a similar resistance to your stock injectors.


With few exceptions, MegaSquirt EMS is legal for use on off road or race use vehicles only.