The 47-year-old had been interim manager alongside Matty Dolan since February, which saw them oversee an impressive upturn in form.
They made an unexpected push for the play-offs, but ending up missing out, finishing 10th in the table, five points from the final spot.
Miller has been awarded for his work, taking up a permanent role as manager ahead of the 2026/27 season.
He has previously been the manager of the Moors, having had a spell back in 2021, but was sacked after seven months in charge.
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Since then, the former goalscoring midfielder has worked as an assistant manager at fellow seventh tier sides Buxton and South Shields.
Miller was a fans’ favourite during his spell at Portman Road, making more than 200 appearances for Town over two stints, scoring 47 goals.