Quantifying the effects of ocean acidification requires understanding the skeletal carbonate mineralogy in living marine organisms. X-ray diffractometry (XRD) is the simplest and most commonly used technique for determining this. Samples being analyzed by XRD are typically pretreated to remove organic material prior to grinding to a crystallite powder. This pretreatment was traditionally performed as organic material may obscure the mineral peaks on XRD traces. This study compared controls with no pretreatment with the most common pretreatment methods: roasting, immersion in chlorine bleach, and immersion in hydrogen peroxide. The latter two methods were performed at two strengths and two durations. We test the hypothesis that bleaching and/or roasting of skeletal carbonate to remove organic material does not affect the mineralogy of temperate skeletal carbonate at a scale detectable by XRD. This was done with biogenic skeletal carbonate from temperate marine environments around southern New Zealand. Specimens included 5 species of bivalve mollusks, 4 species of bryozoans, 2 species of barnacles, as well as 1 species each of serpulid worm, echinoid, gastropod mollusk, brachiopod, and coralline algae. Comparison to the untreated control showed that all pretreatments removed some organic matter and that the presence of organic matter in temperate skeletal carbonate does not affect the ability to qualitatively interpret mineralogy or semiquantitatively measure mineralogy using XRD. Given that pretreatment does not appear to be necessary and that some methods at least can cause unacceptable changes in mineralogy, we recommend that pretreatment for the removal of organic material be abandoned.