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My alternator is undercharging the battery

I bought a new used car that came with an after market stereo system. It appears that whoever owned the car before me removed the amp and subwoofer. Now all that remains is a basic 50 watt amp in the dashboard headend. But they left behind a 1 farad capacitor underneath the passenger seat. When I first got the car, my alternator was overcharging the battery by quite a bit. So I had that replaced. But now, with the new alternator, it slightly undercharges when the A/C, lights and radio and other electrical systems are running. My question is this: Is the capacitor putting too much stress on the new alternator? I suspect that the reason the previous alternator was overcharging the battery was because the previous owner installed a bigger alternator to power the bigger stereo system. But without the amp and sub, this bigger alternator overcharged the system. Now that there’s a smaller alternator, I’m slightly undercharging. I suspect that if I remove the capacitor, that might solve the problem since it won’t be taxing the alternator anymore. Am I correct?

The first thing I would like to say is you have to be very careful with that capacitor.
Mishandling can be dangerous.

How do you know it is undercharging? What symptoms are you seeing.

I know because every now and then the battery light would flash on for a split second. I took it to my mechanic and they measured the output and found that it was slightly undercharging when all the electrical systems were running. So they assumed they had installed a bad alternator and put a new one on. But the next day, the light started flickering on. I think it’s very unlikely I’d get two bad alternators in a row which is why I suspect that this capacitor might be overtaxing the alternator a little bit.

And yes - I have no intention of disconnecting the capacitor by myself, I’d have a professional do it. Thanks!

A larger alternator should not overcharge the battery even with the amp and sub removed.

There’s a lot of missing info.
How was it determined that the battery was being overcharged by quite a bit?
What were the symptoms?

With the undercharging what are the symptoms?
Dimming lights at idle, battery not staying fully charged, or what?

There are several things that can cause an alternator light to flash on. Poor connection at the alternator plug, poor connection at a battery terminal or fusible link end, etc.
So has the belt that drives the alternator been inspected to verify that it’s not slipping?

If there’s any question about how much of an electrical load is being consumed by the car’s electrics then that can be easily checked and should have been done when the alternator was replaced.
It’s unknown to me as to how the alternator was tested for this undercharge condition but it involves more than throwing a voltmeter on it.

they measured the output and that’s how they knew it was overcharging. Also, the lights were wavering in brightness when it was overcharging.

With the undercharging, there are no symptoms other than the flickering light. There are no dimming lights or anything like that. They replaced the alternator a second time and the problem returned the next day - these guys always do good work, so I trust that they hooked it up properly. I don’t know though if the belt has been inspected, so that might be something to look into.

If the light is flickering when you are driving the car other than idling,then I would suspect the belt or a bad connection.

If it flickers while idling, then what may be happening is that the engine could be dropping it’s idle speed a little to cause this or the idle is to low.

From your statements about the first alternator it sounds like some of the diodes were bad in it and possibly the voltage regulator. As for the problem with the replacement it would be good to know where the techs checked the voltage at. There may be some excessive wire connection loss between the alternator output connection and the battery. Checking for a voltage drop between those points would tell the story. There should be less than .1 volt between those points with a good load on the system. The alternator should be generating at least 14.25 volts while the engine is running around 2,000 RPM.

As far as the capacitor is concerned it shouldn’t be a problem. Once a capacitor charges up it stays charged so no real load on the system. You can disconnect it if you want to. Just don’t short the connections. You will need to disconnect the wiring to it also since that will be tied to power. If you can find the fuse for the circuit you could just pull it out. There is only 12 volts going to the cap so it isn’t going to shock you. If you do remove it then you should discharge it also. By tieing something like a brake light bulb across the connections it will safely discharge the cap.

Big power use in the car might mean that you have to improve the ground. The best way is to make up a ground wire from the engine to the fender. This helps, no matter where the problem is. If the engine isn’t well grounded to the body or the body isn’t well grounded to the battery you will improve it. Sometimes it’s enough to keep the warning light off.

Flickering lights is likely to be something other than the alternator; belt slipping, fusible link wire end connection, alternator to battery wire connection, etc.

Without knowing exactly how they tested the alternator and the readings taken I would have no idea what’s going on here.
They’ve replaced the alternator twice in an attempt to cure this so obviously they’re overlooking something.