Abstract Although the effects of arbuscular mycorrhizal fungi (AMF) on host plants have been well documented, whether the effects of AMF on parental generations affect offspring performance is not fully clear. We conducted a common garden experiment to determine whether AMF status of host plants (Medicago truncatula) affects phenotype and transcriptome expression of their offspring. Seeds from four type parental treatments (low-phosphorus (P) soil without AMF, low-P soil with AMF, high-P soil without AMF and high-P soil with AMF) were grown under low-P (LPS) and normal-P soil (OHS) conditions. The flowering pattern of LP offspring was similar to their parents, such that plants with AMF flowered earlier than those without AMF under OHS condition but were opposite under LPS condition. The transcriptome differential analysis showed that some differential transcripts (45 for parental plants growing under low-P condition and 3 for parental plants growing under high-P condition) expression patterns between offspring were comparable, and that only affected by parental AMF status regardless of the P environment that offspring was grown. Others (146 for parental plants growing under low-P condition and 2 for parental plants growing under high-P condition), however, were affected both by the parental AMF status and the offspring P environment. In addition, the number of differential transcripts between offspring whose parental plants grew under high-P condition was far less than under low-P condition. These results indicate that AMF may not only affect the current generation of host plants but also affect the offspring especially when their parents have experienced a stressful environment.