Background: The purpose of this study was to examine the effects of Structured Word Inquiry (SWI; an orthography intervention with a focus on morphology and how morphology interrelates with phonology and etymology) and Simplicity intervention (a novel phonics intervention) on the reading and spelling skills of persistently poor Grade 3 readers. Methods: Forty-eight English-speaking Canadian children (19 females, M[subscript age] = 8.73 years) with persistent reading difficulties were randomly assigned to one of three conditions: SWI, Simplicity and Control. Interventions were delivered by trained graduate students over 10 weeks, 3 times a week, for 30 minutes. Children were tested three times (pre-test, post-test and delayed post-test) on measures of phonological awareness, morphological awareness, reading (Word Reading, Morphological Relatedness and Word Attack) and spelling. Results: Results of hierarchical linear modelling showed a significant main effect of condition for Morphological Relatedness at post-test favouring SWI and Simplicity over Control and a significant interaction between a latent variable of all secondary decoding measures and morphological awareness. Effect sizes (Cohen's "d") showed medium to large effects for both interventions on primary outcomes of Word Reading and Morphological Relatedness. Conclusions: These findings suggest that SWI and Simplicity can help persistently poor readers improve in some reading skills, but neither programme is a panacea as a number of children continued to struggle after the intervention.