This dataset encompass soil microbial assemblages (16S rRNA soil and 18S soil) and nematode-associated microbiomes (16S rRNA nematodes) collected at both compacted and uncompacted soil habitats in the Shipley Skinner Reserve, CA, USA. Desert habitats included coastal sage scrub, chaparral, and native grass for compacted soils holly-leaf cherry, oak woodland, and riparian for uncompacted soils. Samples (soil, host-associated microbiomes, blanks, and controls) were sequencing using the Illumina MiSeq Platform (2x300-bp paired-end). Thus, each sample in this dataset is represented by an R1 and R2 fastq file.