Difficulties in implementing effective instruction for at-risk students arise from two challenges: the transfer of evidence-based knowledge and the lack of economic resources. Computer-assisted programmes offer a suitable solution, providing quality instruction using low-cost resources. Thirty-two first-grade students with early learning difficulties were identified and paired based on at least three of the pre-intervention reading measures (reading efficiency of monosyllabic and disyllabic items, words, pseudowords and text reading speed). Each pair was assigned to one of two different intervention programmes: a computer-assisted intervention programme (CAIP) focused on syllables or the programme provided by the Spanish State School Assistance Services (SSAS). Every week, the CAIP participants received in pairs four 15-min training sessions on syllable decoding plus one 30-min group comprehension session. The CAIP was delivered by trainee students. The SSAS programme typically consisted of a 1-hr individual or in small groups sessions per week delivered by trained practitioners. Both programmes were administered for 11 weeks. The CAIP intervention showed better results than the SSAS intervention for both decoding and comprehension, with moderate to large effect sizes.