Colorectal cancer (CRC) screening is underutilized, especially in low income, high minority populations. We examined the effect test-specific barriers have on colonoscopy and fecal immunochemical test (FIT) completion, what rationales are given for non-completion, and what "switch" patterns exist when participants are allowed to switch from one test to another. Low income adults who were not up-to-date with CRC screening guidelines were recruited from safety-net clinics and offered colonoscopy or FIT (n = 418). Follow up telephone surveys assessed test-specific barriers. Test completion was determined from patient medical records. For subjects who desired colonoscopy at baseline, finding a time to come in and transportation applied more to non-completers than completers (p = 0.001 and p < 0.001, respectively). For participants who initially wanted FIT, keeping track of cards, never putting stool on cards, and not remembering to mail cards back applied more to non-completers than completers (p = 0.003, p = 0.006, and p < 0.001, respectively). The most common rationale given for not completing screening was a desire for the other screening modality: 7 % of patients who initially preferred screening by FIT completed colonoscopy, while 8 % of patients who initially preferred screening by colonoscopy completed FIT. We conclude that test-specific barriers apply more to subjects who did not complete CRC screening. As a common rationale for test non-completion is a desire to receive a different screening modality, our findings suggest screening rates could be increased by giving patients the opportunity to switch tests after an initial choice is made.