I am using the MCP73831 along with a Lithium Ion battery to supply an Arduino Mini project. Is it safe to supply my project directly on the battery? Or should I use a transistor to protect the project from the high charging voltage? Please mind that I need to keep the power consumption at a minimum for this project.
When I understand you right, you want to know whether you can connect your project directly to the battery, even when the battery is charged? The answer is somewhat hidden in the MCP73831 data sheet, on page 13:
during constant-current mode, the programmed charge current is supplied to the battery or the load
So yes, your project can be connected to the battery all the time. When you connect the power supply to the charging circuit, your project will be powered by it.
The current your project needs gets subtracted from the charging current (that means the battery will be charged at a lower rate)
Likewise, when your project needs more current than you have programmed as charging current, the battery will need to supply the additional current.
During charging, your project will be powered by the charging voltage, which will be at most 4.2 volts (OK, maybe 4.5 volts when your battery needs this), so you will be on the safe side with the Arduino Mini.
Since single cell lipo batteries are charged no higher than 4.2V (nor does the voltage exceed this level during charging) there should be no danger in powering most micro controllers from them directly. I'm not sure what you mean by transistor protection, mind elaborating?
The datasheet on page 13 states "during constant-current mode, the programmed charge current is supplied to the battery or the load". I would suggest that it's NOT safe for the MCP73831 to supply both battery and load.
The problem is that, when the MCP73831 reaches the constant voltage mode, the current would never drop to the 10% of the programmed charge current as required to terminate the charge because the current drawn by the load circuit would keep it above the 10%. As a result, the LiPo would be constantly on charge at the 4.2v level.