The PAU Survey studies the existence and properties of dark energy from the observations of redshift space distortions and weak lensing magnification from galaxy cross-correlations as main cosmological probes. The PAU Team is building an instrument, PAUCam, equipped with fully depleted CCD detectors, designed to be mounted at the prime focus of the 4.2 m diameter William Herschel Telescope (WHT) in La Palma. Simulations indicate that PAUCam at the WHT will be able to image about 2 square degrees per night in 40 narrow-band filters plus six wide-band filters to an AB magnitude depth of i ∼ 22.5, providing low-resolution (R ∼ 50) photometric spectra for around 30,000 galaxies, 5,000 stars and 1,000 quasars per square degree. Accurate photometric calibration of the PAU data is vital to achieve the survey science goals. This calibration is challenging due to the large and unusual filter set. We outline the data management pipelines being developed for the survey, both for nightly data reduction and co-addition of multiple epochs, with emphasis on the photometric calibration strategies. We also describe the main tests and results in the characterization of our Hamamatsu fully depleted detectors.