Many of the world’s productive Jurassic reservoirs are intensively bioturbated, including the sediments of the Upper Jurassic Hanifa Formation. Hydrocarbon exploration and production from such reservoirs require a reliable prediction of petrophysical properties (i.e., porosity, permeability, acoustic velocity) by linking and assessment of ichnofabrics and trace fossils and determining their impact on reservoir quality. In this study, we utilized outcrop carbonate samples from the Hanifa Formation to understand the main controlling factors on reservoir quality (porosity and permeability) and acoustic velocity of bioturbated carbonates, by using thin-section petrography, SEM, XRD, CT scan, porosity, permeability, and acoustic velocity measurement. The studied samples are dominated by Thalassinoides burrows that have burrow intensity ranging from ~4% to 27%, with porosity and permeability values ranging from ~1% to 20%, and from 0.002 mD up to 1.9 mD, respectively. Samples with coarse grain-filled burrows have higher porosity (average µ = 14.44% ± 3.25%) and permeability (µ = 0.56 mD ± 0.55) than samples with fine grain-filled burrows (µ = 6.56% ± 3.96%, and 0.07 mD ± 0.16 mD). The acoustic velocity is controlled by an interplay of porosity, bioturbation, and mineralogy. Samples with relatively high porosity and permeability values (>10% and >0.1 mD) have lower velocities (<5 km/s) compared to tight samples with low porosities and permeabilities (<10% and 10% quartz content) show lower velocities compared to the samples with lower quartz content. Bioturbation intensity, alone, has no control on velocity, but when combined with burrow fill, it can be easier to discriminate between high and low velocity samples. Fine grain-filled burrows have generally lower porosity and higher velocities (µ = 5.46 km/s) compared to coarse grain-filled burrows (µ = 4.52 km/s). Understanding the main controlling factor on petrophysical properties and acoustic velocity of bioturbated strata can enhance our competency in reservoir quality prediction and modeling for these bioturbated units.