Op-amp input stage for Arduino Due ADC - guitar signal
Many problems:

You forgot to power the opamp!  This is not a rail to rail opamp, so the power scheme needs to be thought about carefully.

You say you have a non-inverting amp followed by a active filter, but that is not what the schematic shows.  Both stages are clearly inverting.

You mention a 3.3 V supply, but then the schematic shows a battery used only for setting the bias point of the first amp.  This seems needlessly complex and klunky.  It would be simpler to use the 3.3 V supply directly to derive the bias voltage from.  The TL081 has very high input impedance, so this could be a voltage divider drawing only a few &micro;A, which wouldn't put any meaninful burden on the existing supply.

The bias voltage divider is correct for a 9 V source, but "9 V" batteries vary a bit.  The error scaled down to half of 3.3 V shouldn't cause too much trouble, but why use a separate voltage source and then divide it down to try to match 1/2 the supply?  It makes more sense to use the supply itself with two equal resistors, like 100 k&Omega; each, to make the bias voltage.  See point 3, above.

The second amp is biased at 0 with a DC gain of -1.  That will produce negative output voltages, which is unlikely what you want.

The low pass fillter has about 10 kHz rolloff.  That implies a sample rate of 10s of kHz unless you know something special about the frequency content of the signal.  Do you really intend to sample at 50 kHz or so?